genetika

London BioGeeks | Bioinformatics in London | Page 2

2011-01-06T08:16:00.000-08:00

London BioGeeks Bioinformatics in London Page 2: "London BioGeeks
Bioinformatics in London"

DNA sequencing technologies

2010-10-07T02:39:00.000-07:00

DNA sequencing technologies - tutorial on traditional and next-generation sequencing technologies

useful databases, genetic research, LD analysis

2010-10-07T01:55:00.000-07:00

useful databases for genetic research ,

These sites are of potential interests for people carrying out LD analysis:

Nomenclature for the description of sequence variants

2010-10-07T01:10:00.000-07:00

human genetic variation
nomenclature of genetic sequence changes, variants etc

intro R statistical package

2009-10-28T14:55:00.000-07:00

intro courses in R

quick-R - a "must see" by dr Kabacoff,
also preparing book "R in action"

nice tutorial on R- pdf. 104pp by Matloff - Uni Davis

Oxford course by Ruth Ripley incl. slides, r files ....

Aarhus introduction course XXX- recommended books, course materials,
by Ulrich Halekoh, Søren Højsgaard, Asger R. Pedersen incl. R in Few Hours tutorial :)

Intro to R XXX - quite extensive pdf, datamanipulations, graphics, statistics, up to datamining.
by Statgenetics ... UAB ...UofAlabamaATbirmingham by Lumley T /member of R core develepment team
site includes some other pdf of exercise etc, and even video /videos only for Uni-members

Using R for statistical analyses - Introduction by dr Gardener - nice layout

MAT 356 R Tutorial, Spring 2004 - concise, many examples, inclusive plotting options, very instructive

advanced statistics - Exploratory Data Analysis (EDA) and Regression from astrophysicist
- includes a lot of code for different types of regression (linear, polynomial, ridge, spline .....), but no plot, or other output

genetic statistics SOFTWARE

2009-10-28T14:39:00.000-07:00

LINKAGE AND LINKAGE DISEQUILIBRIUM

GENETIC STATISTICS, STATISTICAL GENETICS SOFTWARE
Following are the category of programs we have available for the analysis:
Association and TDT Programs
Error Checking Programs
Genome Wide Association Programs
Haplotyping Programs
Linkage Analysis Programs
Pedigree Drawing Programs
Population Genetics Programs
Segregation Programs
Simulation Programs
Stratification Programs
Utility Programs

linkage disequilibrium

2009-10-28T14:15:00.000-07:00

linkage disequilibrium (LD)- basics, measures /D, Dprime, r_squared/, causes, of LD by Abecasis from U Michigan
- includes pros and cons and limitations of individual measures of LD !!!!

linkage disequilibrium - worked example of how to compute different measures, on causes etc.

"classical" brief note on LD - linkage vs linkage disequilibrium

paper on volume measures of LD - as part of intro describes calculation of D´and r2.

statistics resources

2009-10-18T08:34:00.000-07:00

hyperstats - basics - distribution

SOCR - statistcal online computation resource -from UCLA
JAVA applets - distributions - analyses - plots - models - games
check out - links to wiki.

Dallal - Little Handbook of statistical practice
- comprehensible - text-based, includes figures

xanthomas

2009-08-28T16:47:00.000-07:00

Cutaneous xanthomas associated with hyperlipidemia can be classified as
xanthelasma palpebrarum,
tendinous xanthomas,
eruptive xanthomas,
tuberous xanthomas, and
plane xanthomas.

low HDL syndromes

2009-08-11T10:26:00.000-07:00

Tangier disease
Tangier - 9q
- orange tonsils, hepatosplenomegaly, polyneuropathy (syringomyelia-like), premature CVS
- hypoHDL
- ABCA1 mutation, loss-off-function,
- cellular cholesterol efflux impaired

primary familial hypoalfalipoproteinemia OMIM 604091
-French Canadian
- lowHDL, normal TG
- ABCA1 mutation 9q

LCAT deficiency
lecithin-cholesterol acyltransferase OMIM 606967
- soluble enzyme that converts cholesterol and phosphatidylcholines (lecithins) to cholesteryl esters and lysophosphatidylcholines on the surface of high density lipoproteins
'reverse cholesterol transport.' The enzyme is synthesized in the liver and circulates in blood plasma as a complex with components of high density lipoprotein (HDL).
- Cholesterol from peripheral cells is transferred to HDL particles, esterified through the action of LCAT on HDL, and incorporated into the core of the lipoprotein. The cholesterol ester is thereby transported to the liver (Jonas, 2000). A lack of LCAT activity would be expected to lead to accumulation of free cholesterol in the tissues. Most cholesterol esters present in plasma are the product of the reaction catalyzed by LCAT in which cholesterol is esterified with the sn-2 fatty acid of phosphatidylcholine. The resulting cholesteryl esters are packed into the hydrophobic core of lipoproteins.
In fish-eye disease (OMIM 136120), there is a specific inability of LCAT to esterify cholesterol in HDL, a deficiency of alpha-LCAT function. In Norum disease (245900), the deficient esterification is generalized (Kinoshita and Teramoto, 2001).
PATHOGENESIS
Carlson and Holmquist (1985) and Holmquist and Carlson (1987) demonstrated that the defect in fish-eye disease is deficiency of high density lipoprotein lecithin:cholesterol acyltransferase activity.

Alpha-LCAT, deficient in this condition, is specific for HDL, whereas beta-LCAT, also deficient in Norum disease (245900), is specific for combined VLDL and LDL (Carlson and Holmquist, 1985). Thus, fish-eye disease is one form of LCAT deficiency. In fish-eye disease, the HDL of plasma contains only about 20% cholesteryl esters relative to total cholesterol as compared to 75 to 80% in control HDL. In fish-eye disease plasma, however, there is a normal cholesteryl ester percentage as well as a normal plasma cholesterol esterification rate as a result of the activity of beta-LCAT.

dm2 prediction

2009-07-04T11:40:00.000-07:00

Multiple biomarker prediction of type 2 diabetes.
Meigs JB.

van Hoek DM2 prediction in population study Rotterdam

Joint Effects of Common Genetic Variants on the Risk for Type 2 Diabetes in U.S. Men and Women of European Ancestry Marilyn C. Cornelis, PhD; Lu Qi, MD, PhD; Cuilin Zhang, MD, PhD; Peter Kraft, PhD; JoAnn Manson, MD, DPH; Tianxi Cai, PhD; David J. Hunter, MBBS, ScD; and Frank B. Hu, MD, PhD
21 April 2009 Volume 150 Issue 8 Pages 541-550
Conclusion: Although its discriminatory value is currently limited, a GRS that combines information from multiple genetic variants might be useful for identifying subgroups with a particularly high risk for type 2 diabetes.
annal of internal medicine- NURSES HEALTH STUDY

Comment in:
Lancet. 2009 Jun 27;373(9682):2178-9.
Trajectories of glycaemia, insulin sensitivity, and insulin secretion before diagnosis of type 2 diabetes: an analysis from the Whitehall II study.
Tabák AG, Jokela M, Akbaraly TN, Brunner EJ, Kivimäki M, Witte DR.
INTERPRETATION: In this study, we show changes in glucose concentrations, insulin sensitivity, and insulin secretion as much as 3-6 years before diagnosis of diabetes. The description of biomarker trajectories leading to diabetes diagnosis could contribute to more-accurate risk prediction models that use repeated measures available for patients through regular check-ups.

Using the Optimal Receiver Operating Characteristic Curve to Design a Predictive Genetic Test, Exemplified with Type 2 Diabetes
Qing Lu1 and Robert C. Elston1

CF SERIES OF BASIC EPIDEMIOLOGY/STATISTCS BY AKOBENG
/DIAGNOSTIC TESTS/ UIN ACTA PAEDIATRICA

CALIBRATION STATISTICS
CF DIAGNOSTIC VS PROGNOSTIC MODELS - ROC

Cook NR. Statistical evaluation of prognostic versus diagnostic models: beyond the ROC curve. Clin Chem 2008;54:17-23. [Free Full Text]

Fine-tuning of prediction of isolated impaired glucose tolerance: a quantitative clinical prediction model.
Rambod M, Hosseinpanah F, Ardakani EM, Padyab M, Azizi F.
Diabetes Res Clin Pract. 2009 Jan;83(1):61-8. Epub 2008 Nov 13.
PMID: 19012984 [PubMed - indexed for MEDLINE]
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ARIC STUDY
Comment in:
Ann Intern Med. 2009 Jun 2;150(11):812-4.
Two risk-scoring systems for predicting incident diabetes mellitus in U.S. adults age 45 to 64 years.
Kahn HS, Cheng YJ, Thompson TJ, Imperatore G, Gregg EW.
Centers for Disease Control and Prevention, 4770 Buford Highway Northeast, Atlanta, GA 30341, USA.
CONCLUSION: Basic information identified adults at high risk for diabetes. Additional data from fasting blood tests better identified those at extreme risk.
RESULTS: The basic scoring system included waist circumference (10 to 35 points); maternal diabetes (13 points); hypertension (11 points); and paternal diabetes, short stature, black race, age 55 years or older, increased weight, rapid pulse, and smoking history (< or ="8" or ="7" href="http://www.bmj.com/cgi/content/full/338/mar17_2/b880?view=long&pmid=19297312">Predicting risk of type 2 diabetes in England and Wales: prospective derivation and validation of QDScore

Different strategies for screening and prevention of type 2 diabetes in adults: cost effectiveness analysis
Clare L Gillies, Paul C Lambert, Keith R Abrams, Alex J Sutton, Nicola J Cooper, Ron T Hsu, Melanie J Davies, and Kamlesh KhuntiBMJ 2008 336: 1180-1185. [Abstract] [Full Text] [

Impaired fasting glucose cutoff value of 5.6 mmol/l combined with other cardiovascular risk markers is a better predictor for incident Type 2 diabetes than the 6.1 mmol/l value: Tehran lipid and glucose study.
Harati H, Hadaegh F, Tohidi M, Azizi F.
Diabetes Res Clin Pract. 2009 Jul;85(1):90-5. Epub 2009 May 2.
PMID: 19414206 [PubMed - in process]
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Serum uric acid levels improve prediction of incident type 2 diabetes in individuals with impaired fasting glucose: the Rancho Bernardo Study.
Kramer CK, von Mühlen D, Jassal SK, Barrett-Connor E.
Diabetes Care. 2009 Jul;32(7):1272-3. Epub 2009 Apr 14.
PMID: 19366963 [PubMed - in process]
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gattaca are we yet there????

Genome-wide association studies in type 2 diabetes.
McCarthy MI, Zeggini E.
Curr Diab Rep. 2009 Apr;9(2):164-71. Review.
PMID: 19323962 [PubMed - in process]
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Clinical translation of genetic predictors for type 2 diabetes.
Majithia AR, Florez JC.
Curr Opin Endocrinol Diabetes Obes. 2009 Apr;16(2):100-6. Review.
PMID: 19306524 [PubMed - indexed for MEDLINE]
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Construction of a prediction model for type 2 diabetes mellitus in the Japanese population based on 11 genes with strong evidence of the association.
Miyake K, Yang W, Hara K, Yasuda K, Horikawa Y, Osawa H, Furuta H, Ng MC, Hirota Y, Mori H, Ido K, Yamagata K, Hinokio Y, Oka Y, Iwasaki N, Iwamoto Y, Yamada Y, Seino Y, Maegawa H, Kashiwagi A, Wang HY, Tanahashi T, Nakamura N, Takeda J, Maeda E, Yamamoto K, Tokunaga K, Ma RC, So WY, Chan JC, Kamatani N, Makino H, Nanjo K, Kadowaki T, Kasuga M.
J Hum Genet. 2009;54(4):236-41. Epub 2009 Feb 27.
PMID: 19247372 [PubMed - in process]

Prediction of type 2 diabetes using alternate anthropometric measures in a multi-ethnic cohort: the insulin resistance atherosclerosis study.
MacKay MF, Haffner SM, Wagenknecht LE, D'Agostino RB Jr, Hanley AJ.
Diabetes Care. 2009 May;32(5):956-8. Epub 2009 Feb 5.
PMID: 19196891 [PubMed - in process]
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Prediction of type 2 diabetes using simple measures of insulin resistance: combined results from the San Antonio Heart Study, the Mexico City Diabetes Study, and the Insulin Resistance Atherosclerosis Study.
Hanley AJ, Williams K, Gonzalez C, D'Agostino RB Jr, Wagenknecht LE, Stern MP, Haffner SM; San Antonio Heart Study; Mexico City Diabetes Study; Insulin Resistance Atherosclerosis Study.
Diabetes. 2003 Feb;52(2):463-9. Erratum in: Diabetes. 2003 May;52(5):1306.
PMID: 12540622 [PubMed - indexed for MEDLINE]
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Use of alternative thresholds defining insulin resistance to predict incident type 2 diabetes mellitus and cardiovascular disease.
Rutter MK, Wilson PW, Sullivan LM, Fox CS, D'Agostino RB Sr, Meigs JB.
Circulation. 2008 Feb 26;117(8):1003-9. Epub 2008 Feb 4.
PMID: 18250267 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC at journal site

M. A. Abdul-Ghani, V. Lyssenko, T. Tuomi, R. A. DeFronzo,
and L. Groop
Fasting Versus Postload Plasma Glucose Concentration and the Risk for Future Type 2 Diabetes: Results from the Botnia Study Diabetes Care February 1, 2009 32:281-286
Abstract Full Text Full Text (PDF)

S. Prudente, D. Scarpelli, M. Chandalia, Y.-Y. Zhang, E. Morini, S. Del Guerra, F. Perticone, R. Li, C. Powers, F. Andreozzi, P. Marchetti, B. Dallapiccola, N. Abate, A. Doria, G. Sesti,
and V. Trischitta
The TRIB3 Q84R Polymorphism and Risk of Early-Onset Type 2 Diabetes Journal of Clinical Endocrinol January 1, 2009 94:190-196
Abstract

Is femur length the key height component in risk prediction of type 2 diabetes among adults?
Liu J, Tan H, Jeynes B.
Diabetes Care. 2009 Apr;32(4):739-40. Epub 2009 Jan 26.
PMID: 19171722 [PubMed - in process]
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Risk prediction of prevalent diabetes in a Swiss population using a weighted genetic score--the CoLaus Study.
Lin X, Song K, Lim N, Yuan X, Johnson T, Abderrahmani A, Vollenweider P, Stirnadel H, Sundseth SS, Lai E, Burns DK, Middleton LT, Roses AD, Matthews PM, Waeber G, Cardon L, Waterworth DM, Mooser V.
Diabetologia. 2009 Apr;52(4):600-8. Epub 2009 Jan 13.
PMID: 19139842 [PubMed - indexed for MEDLINE]
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Combined measurement of fasting plasma glucose and A1C is effective for the prediction of type 2 diabetes: the Kansai Healthcare Study.
Sato KK, Hayashi T, Harita N, Yoneda T, Nakamura Y, Endo G, Kambe H.
Diabetes Care. 2009 Apr;32(4):644-6. Epub 2009 Jan 8.
PMID: 19131461 [PubMed - in process]
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Use of HbA1c in predicting progression to diabetes in French men and women: data from an Epidemiological Study on the Insulin Resistance Syndrome (DESIR).
Droumaguet C, Balkau B, Simon D, Caces E, Tichet J, Charles MA, Eschwege E; DESIR Study Group.
Diabetes Care. 2006 Jul;29(7):1619-25.
PMID: 16801588 [PubMed - indexed for MEDLINE]
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Comparison of a clinical model, the oral glucose tolerance test, and fasting glucose for prediction of type 2 diabetes risk in Japanese Americans.
McNeely MJ, Boyko EJ, Leonetti DL, Kahn SE, Fujimoto WY.
Diabetes Care. 2003 Mar;26(3):758-63.
PMID: 12610034 [PubMed - indexed for MEDLINE]
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Fasting versus postload plasma glucose concentration and the risk for future type 2 diabetes: results from the Botnia Study.
Abdul-Ghani MA, Lyssenko V, Tuomi T, DeFronzo RA, Groop L.
Diabetes Care. 2009 Feb;32(2):281-6. Epub 2008 Nov 18.
PMID: 19017778 [PubMed - indexed for MEDLINE]
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SKIN AUTOFLUORESCENCE
Noninvasive type 2 diabetes screening: superior sensitivity to fasting plasma glucose and A1C.
Maynard JD, Rohrscheib M, Way JF, Nguyen CM, Ediger MN.
Diabetes Care. 2007 May;30(5):1120-4. Epub 2007 Mar 2.
PMID: 17337498 [PubMed - indexed for MEDLINE]
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HbA1c measurement improves the detection of type 2 diabetes in high-risk individuals with nondiagnostic levels of fasting plasma glucose: the Early Diabetes Intervention Program (EDIP).
Perry RC, Shankar RR, Fineberg N, McGill J, Baron AD; Early Diabetes Intervention Program (EDIP).
Diabetes Care. 2001 Mar;24(3):465-71.
PMID: 11289469 [PubMed - indexed for MEDLINE]
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Screening for type 2 diabetes and impaired glucose metabolism: the Australian experience.
Colagiuri S, Hussain Z, Zimmet P, Cameron A, Shaw J; AusDiab.
Diabetes Care. 2004 Feb;27(2):367-71.
PMID: 14747215 [PubMed - indexed for MEDLINE]
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Diagnostic and therapeutic implications of relationships between fasting, 2-hour postchallenge plasma glucose and hemoglobin a1c values.
Woerle HJ, Pimenta WP, Meyer C, Gosmanov NR, Szoke E, Szombathy T, Mitrakou A, Gerich JE.
Arch Intern Med. 2004 Aug 9-23;164(15):1627-32.
PMID: 15302632 [PubMed - indexed for MEDLINE]
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FINNISH DIABETES RISK SCORE

The Finnish Diabetes Risk Score is associated with insulin resistance and progression towards type 2 diabetes.
Schwarz PE, Li J, Reimann M, Schutte AE, Bergmann A, Hanefeld M, Bornstein SR, Schulze J, Tuomilehto J, Lindström J.
J Clin Endocrinol Metab. 2009 Mar;94(3):920-6. Epub 2008 Dec 23.
PMID: 19106274 [PubMed - indexed for MEDLINE]

NMR-determined lipoprotein subclass profile predicts type 2 diabetes.
Hodge AM, Jenkins AJ, English DR, O'Dea K, Giles GG.
Diabetes Res Clin Pract. 2009 Jan;83(1):132-9. Epub 2008 Dec 16.
PMID: 19091436 [PubMed - indexed for MEDLINE]
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Metabolic syndrome and risk of incident diabetes: findings from the European Prospective Investigation into Cancer and Nutrition-Potsdam Study.
Ford ES, Schulze MB, Pischon T, Bergmann MM, Joost HG, Boeing H.
Cardiovasc Diabetol. 2008 Dec 12;7:35.
PMID: 19077281 [PubMed - indexed for MEDLINE]
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A prediction model for type 2 diabetes risk among Chinese people.
Chien K, Cai T, Hsu H, Su T, Chang W, Chen M, Lee Y, Hu FB.
Diabetologia. 2009 Mar;52(3):443-50. Epub 2008 Dec 5.
PMID: 19057891 [PubMed - indexed for MEDLINE]
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TCF7L2 variant genotypes and type 2 diabetes risk in Brazil: significant association, but not a significant tool for risk stratification in the general population.
Marquezine GF, Pereira AC, Sousa AG, Mill JG, Hueb WA, Krieger JE.
BMC Med Genet. 2008 Dec 4;9:106.
PMID: 19055834 [PubMed - indexed for MEDLINE]
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Tools for predicting the risk of type 2 diabetes in daily practice.
Schwarz PE, Li J, Lindstrom J, Tuomilehto J.
Horm Metab Res. 2009 Feb;41(2):86-97. Epub 2008 Nov 19. Review.
PMID: 19021089 [PubMed - indexed for MEDLINE]
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Clinical risk factors, DNA variants, and the development of type 2 diabetes.
Lyssenko V, Jonsson A, Almgren P, Pulizzi N, Isomaa B, Tuomi T, Berglund G, Altshuler D, Nilsson P, Groop L.
N Engl J Med. 2008 Nov 20;359(21):2220-32.
PMID: 19020324 [PubMed - indexed for MEDLINE]
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159:
Genotype score in addition to common risk factors for prediction of type 2 diabetes.
Meigs JB, Shrader P, Sullivan LM, McAteer JB, Fox CS, Dupuis J, Manning AK, Florez JC, Wilson PW, D'Agostino RB Sr, Cupples LA.
N Engl J Med. 2008 Nov 20;359(21):2208-19. Erratum in: N Engl J Med. 2009 Feb 5;360(6):648.
PMID: 19020323 [PubMed - indexed for MEDLINE]
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Validating the Framingham Offspring Study equations for predicting incident diabetes mellitus.
Nichols GA, Brown JB.
Am J Manag Care. 2008 Sep;14(9):574-80.
PMID: 18778172 [PubMed - indexed for MEDLINE]
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Predicting diabetes: clinical, biological, and genetic approaches: data from the Epidemiological Study on the Insulin Resistance Syndrome (DESIR).
Balkau B, Lange C, Fezeu L, Tichet J, de Lauzon-Guillain B, Czernichow S, Fumeron F, Froguel P, Vaxillaire M, Cauchi S, Ducimetière P, Eschwège E.
Diabetes Care. 2008 Oct;31(10):2056-61. Epub 2008 Aug 8.
PMID: 18689695 [PubMed - indexed for MEDLINE]
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Metabolic syndrome and incident diabetes: current state of the evidence.
Ford ES, Li C, Sattar N.
Diabetes Care. 2008 Sep;31(9):1898-904. Epub 2008 Jun 30. Review.
PMID: 18591398 [PubMed - indexed for MEDLINE]
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The interaction between impaired acute insulin response and insulin resistance predict type 2 diabetes and impairment of fasting glucose: report from a 20-year follow-up in the Uppsala Longitudinal Study of Adult Men - ULSAM.
Zethelius B, Berglund L, Hänni A, Berne C.
Ups J Med Sci. 2008;113(2):117-30.
PMID: 18509807 [PubMed - indexed for MEDLINE]
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Validation of prediction of diabetes by the Archimedes model and comparison with other predicting models.
Stern M, Williams K, Eddy D, Kahn R.
Diabetes Care. 2008 Aug;31(8):1670-1. Epub 2008 May 28.
PMID: 18509203 [PubMed - indexed for MEDLINE]
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Insulin-like growth factor-binding protein-1 in the prediction and development of type 2 diabetes in middle-aged Swedish men.
Lewitt MS, Hilding A, Ostenson CG, Efendic S, Brismar K, Hall K.
Diabetologia. 2008 Jul;51(7):1135-45. Epub 2008 May 22.
PMID: 18496669 [PubMed - indexed for MEDLINE]
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305:
Additional contribution of emerging risk factors to the prediction of the risk of type 2 diabetes: evidence from the Western New York Study.
Stranges S, Rafalson LB, Dmochowski J, Rejman K, Tracy RP, Trevisan M, Donahue RP.
Obesity (Silver Spring). 2008 Jun;16(6):1370-6. Epub 2008 Mar 20.
PMID: 18356828 [PubMed - indexed for MEDLINE]
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Adipokines and incident type 2 diabetes in an Aboriginal Canadian [corrected] population: the Sandy Lake Health and Diabetes Project.
Ley SH, Harris SB, Connelly PW, Mamakeesick M, Gittelsohn J, Hegele RA, Retnakaran R, Zinman B, Hanley AJ.
Diabetes Care. 2008 Jul;31(7):1410-5. Epub 2008 Mar 13. Erratum in: Diabetes Care. 2008 Aug;31(8):1713.
PMID: 18339973 [PubMed - indexed for MEDLINE]
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The metabolic syndrome as a tool for predicting future diabetes: the AusDiab study.
Cameron AJ, Magliano DJ, Zimmet PZ, Welborn TA, Colagiuri S, Tonkin AM, Shaw JE.
J Intern Med. 2008 Aug;264(2):177-86. Epub 2008 Feb 20.
PMID: 18298479 [PubMed - indexed for MEDLINE]
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LIVER ENZYMES
Liver enzymes and risk of diabetes and cardiovascular disease: results of the Firenze Bagno a Ripoli (FIBAR) study.
Monami M, Bardini G, Lamanna C, Pala L, Cresci B, Francesconi P, Buiatti E, Rotella CM, Mannucci E.
Metabolism. 2008 Mar;57(3):387-92.
PMID: 18249212 [PubMed - indexed for MEDLINE]
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Determinants of new-onset diabetes among 19,257 hypertensive patients randomized in the Anglo-Scandinavian Cardiac Outcomes Trial--Blood Pressure Lowering Arm and the relative influence of antihypertensive medication.
Gupta AK, Dahlof B, Dobson J, Sever PS, Wedel H, Poulter NR; Anglo-Scandinavian Cardiac Outcomes Trial Investigators.
Diabetes Care. 2008 May;31(5):982-8. Epub 2008 Jan 30.
PMID: 18235048 [PubMed - indexed for MEDLINE]
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Can self-rated health scores be used for risk prediction in patients with type 2 diabetes?
Hayes AJ, Clarke PM, Glasziou PG, Simes RJ, Drury PL, Keech AC.
Diabetes Care. 2008 Apr;31(4):795-7. Epub 2008 Jan 9.
PMID: 18184900 [PubMed - indexed for MEDLINE]
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Impact of common type 2 diabetes risk polymorphisms in the DESIR prospective study.
Vaxillaire M, Veslot J, Dina C, Proença C, Cauchi S, Charpentier G, Tichet J, Fumeron F, Marre M, Meyre D, Balkau B, Froguel P; DESIR Study Group.
Diabetes. 2008 Jan;57(1):244-54. Epub 2007 Oct 31.
PMID: 17977958 [PubMed - indexed for MEDLINE]
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A simplified Finnish diabetes risk score to predict type 2 diabetes risk and disease evolution in a German population.
Bergmann A, Li J, Wang L, Schulze J, Bornstein SR, Schwarz PE.
Horm Metab Res. 2007 Sep;39(9):677-82.
PMID: 17846976 [PubMed - indexed for MEDLINE]
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R quick

2009-06-23T16:28:00.000-07:00

quickR - introduction blog
combining plots

2009-06-08T16:00:00.000-07:00

statistical resources - course notes, materilas, Ingo Ruczinski John Hopkins university

GOODNESS OF FIT, lack of fit test, statistics

2009-06-08T14:02:00.000-07:00

biostatistical genetics and genetic epidemiology by Elston
-- GOODNESS OF FIT

lack of fit test
XXXXX NIST

with examples in R in pdf

Model selection in ecology Johnson 2004 REVIEW PDF

genetic models CLARIFICATIONS NEEDED

2009-05-31T11:30:00.000-07:00

KEYWORDS TO BE CLARIFIED

allelic association, genotypic association (PLINK)

genotype relative risk

allele risk

genetic models = diallelic polymorphisms:

dominant

recessive

co-dominant

overdominant

additive (log-additive)

multiplicative

cf PLINK tutorial section Association

cf Moreno et al. SNPstats

cf Lewis 2002: Genetic association studies: design, analysis interpretation.

cf Handbook of Statistical genetics. Eds. Balding, Bishop ...: chapters 36, 37 by Clayton, and Morris/Cardon

cf SNPGWA tutorial - gives exact documentation for calculations. explains CochranArmitage TREND TEST for log-additive genetic/inheritance model. involves NEWTON-RAPHSON algorithm /iterative process/ simply --- complicated

cf summarize - assumptions of HWE for allelic multiplicative, genotypic tests??

-

can log-additive be computed in SPSS

cf coding recommendations by CLAYTON, Morris -- logistic reg model including ADDITIVE and DOMINANCE factor.

- furthermore - cf likelihood ratio tests for model selection, cf Moreno aIC, BIC...

cf MODELS for binary data /disease status/ and for quantitative phenotypes.

confidence intervals, odds ratio

2009-05-31T09:28:00.000-07:00

general intro on confidence intervals by Steve Simon /children mercy

odds ratio and confidence interval calculation XXX

GENETIC EPIDEMIOLOGY BASICS

2009-05-27T16:05:00.001-07:00

https://courses.washington.edu/b516/lectures/handout9.pdf

Genotypic and Allelic Association for Binary traits TUTORIAL IN STATA

ODDS RATIO IN association testing - includes worked example, incl. formula for 95CI calculation /Woolf

genetic ANALYSIS OF complex disease GOOGLEBOOK

GENETIC ASSOCIATION STUDIES EXPLAINED - A PRIMER

ELEMENTARY CLASSICAL GENETICS

/ASSOCIATION TESTING Rpackage by clayton

hardy weiberg equilibrium, population genetics

2009-04-20T14:29:00.000-07:00

Online Encyclopedia for Genetic Epidemiology
nice resource but seems to lack updates since 2007 ___???
inclued tool for HWE calculation ˇ(but doesn t provide exact p values)

DORAK POPGEN XXXXXXXX ______XXXXXXX
extensive collection of text on genetics, genetic epidemiology, genetic statistics etc (as mentioned repeatedly in this blog)
slight disadvantage - layout is rather poor. lumps of text
- nice addition - music notes

Michael Court excel template for HWE calculation. simple. works fine
www.tufts.edu/~mcourt01/Documents/Court%20lab%20-%20HW%20calculator.xls

evolutionary statistics - evomaths HWE test principle explained

http://de.wikipedia.org/wiki/Hardy-Weinberg-Gleichgewicht DEUTSCH
includes letter by Hardy to Editor of Science: "I am reluctant to intrude in a discussion concerning matters of which I have no expert knowledge, and I should have expected the very simple point which I wish to make to have been familiar to biologists."""

eine schoene erläuterung von Hardy-Weinberg-Gleichgewicht DEUTSCH PPT

Hardy Weinberg EQUILIBRIUM explained .... from Kimballs Biology pages NICE

populační genetika CZECH vedecko populárny resp. pre gymnazia

HWE, theory _ calculation applet + explanation /danish author NICE . population genetics

aktualni genetika Šeda, Šedová Liška, - vybrané kapitoly z lékarskej genetiky, genomiky, biologie.

sim8 applet for allele frequencie, HWE, allele frequencies based on different evolutionary and biological factors -- COMPLICATED

pharmacogenomics database EXTRACTION

2009-03-31T13:58:00.000-07:00

http://www.pharmgkb.org/search/pathway/anti-diabetic/anti-diabetic-pd.jsp#tabview=tab0

MTNR1B rs10830962 PROKOPENKO

2009-03-31T13:32:00.000-07:00

PROKOPENKO

STAIGER 2009

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?showRare=on&chooseRs=all&locusId=4544&mrna=NM_005959.3&ctg=NT_008984.17&prot=NP_005950.1&orien=forward&refresh=refresh

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=snp&Cmd=Link&LinkName=snp_pubmed_cited&IdsFromResult=12804291

sample size

2009-01-21T13:48:00.000-08:00

intro I . in RCT

lancet epidemiology series on sample size samba

physiological statistics by D Sackett

clinical trial simulator

fibrinogen

2009-01-13T08:04:00.000-08:00

FIBRINOGEN ASSAYS GUIDELINES UK 2003

FIBRINOGEN STANDARD 2ND

http://atvb.ahajournals.org/cgi/content/abstract/28/4/758

FIBRINOGEN HAPLOTYPES -NO CAD KOCH2008

GWAS FRAMINGHAM 2007

fibrinogen minutes 2006 XXXXX

ISTH 2008

FBG INTRAINDIVIDUAL VARIABILITY ROUVIER 2002

FIBRINOGEN STUDIES COLLABORATION JAMA 2005

Variability in fibrinogen measurements: an obstacle to cardiovascular risk stratification

rosenson 2001

http://www.clinchem.org/cgi/content/full/50/11/2150

Effect of Specimen Collection on Routine Coagulation Assays and D-Dimer Measurement LIPPI 2004

Among routine coagulation assays, fibrinogen and D-dimer measurements are thought to be more susceptible to variations introduced in the preanalytical phase (2)(3)(4). The term "D-dimer" usually refers to a heterogeneous class of end-stage degradation products of cross-linked fibrin that occur in vivo with a wide range of molecular weights and contain various numbers of the D-dimer motif (5). The strong heterogeneity of D-dimer in plasma might be reflected by most immunoassays (the monoclonal antibodies show variable reactivity with different molecular forms) because the various forms occur naturally in the plasma of patients. This might be particularly true when evaluating D-dimer after continuous blood-sampling because it is conceivable that different samples from the same patients might contain heterogeneous D-dimer isoforms. Some recommended procedures for acquiring samples for coagulation analysis, especially those involving the measurement of D-dimer and fibrinogen by the Clauss method, mandate that the first sample be discarded because tissue thromboplastin released by the trauma of venipuncture could interfere with coagulation assays by activating intrinsic pathway (2). However, in agreement with the earlier report by Rosenson et al. (6), our results demonstrate that a standardized procedure for blood collection does not influence the reliability of in vitro routine coagulation testing. This is particularly true for fibrinogen and D-dimer measurements, as it had been speculated previously that discrepancies might arise from different specimens collected simultaneously from the same patient (2)(6).

atorvastatin on fibrinogen 1998

Immunonephelometric determination of fibrinogen on citrated or heparinized plasma: comparison with functional Clauss method.

As a result, the immunonephelometric method shows reliable performance and clinical sample measurements are not affected by the method used, validating the use of heparinized plasma samples for fibrinogen antigen determination with Dade Behring reagents.

Kinetic Fibrinogen Assay (KFA), a method based on the kinetic reaction of the developing fibrin clot, was used to determine fibrinogen concentration in plasma. Two other methods employing different quantification principles were used for comparison: the von Clauss method and the procedure measuring protein concentration in an isolated and washed plasma clot (World Health Organization [WHO] method). All three methods quantified functional thrombin-coagulable fibrinogen. Tan Am J Clin Path 1995

Comparison of Clauss fibrinogen and fibrinogen measurement derived from aPTT and PT in diabetes mellitus and correlations with markers of glycemic equilibration
Abstract number: P0278
Sobas* F., Hanss† M., Dechavanne* M., Riou* J. P., Drai‡ J., Negrier* C.
‡Centre Hospitalier, Lyon, France *Hôpital Edouard Herriot, Lyon, France; †Hop Cardiologique Lyon, France;
The consequences of fibrinogen glycosylation on fibrinogen polymerization are controversial in the literature. We have compared fibrinogen levels determined with Clauss, prothrombin time derived measurement of fibrinogen (PTd) and activated partial prothrombin time-derived measurement of fibrinogen (aPTTd) in 32 diabetic patients (Sobas et al. Blood Coagul Fibrinolysis, 2002; 13: 61–68) (7 type II and 10 type I diabetic patients without clinical complication, 11 type II and 4 type I diabetic patients with clinical complications, all patients presenting normal range of PT, aPTT and fibrinogen level). We have also correlated the differences between Clauss and derived methods with markers of glycemic equilibration such as glycemia, capillary glucose value and levels of hemoglobin A1C and fructosamine. All coagulation assays (PT, aPTT, Clauss fibrinogen) were performed on an MDA II coagulometer (bioMérieux). To allow comparison of fibrinogen measurements in diabetic samples (Clauss vs. PTd and aPTTd) reference curves were constructed from 30 control plasmas with normal range of PT, aPTT and fibrinogen level. In all the diabetic patients, fibrinogen was lower when using PTd and aPTTd measurements vs. the Clauss method (paired t-test for PTd: mean of differences = -0.49, P < 0.0001; for aPTTd: mean of differences = -0.39, P < 0.0001). In the 18 type II diabetic patients, there are significant correlation between (PTd-Clauss) difference and Glycemia (P = 0.013); Capillary glucose value (P = 0.008) and Haemoglobin A1C (P = 0.031). In the 14 type I diabetic patients, no correlation is observed. In the 11 type II diabetic patients with complications, no correlation is observed. In the 7 type II diabetic patients without complication (PTd-Clauss) difference is correlated with Glycemia (P = 0.034), with Capillary glucose value (P < 0.001) and with hemoglobin A1C (P = 0.023). (aPTTd-Clauss) difference is correlated with fructosamine (P = 0.048) in the 7 type II diabetic patients without complication. The fibrinogen polymerization is abnormal in aPTT and PT tests in diabetic patients when using MDA II coagulometer. The absence of correlation between markers of glycemic equilibration and difference (Clauss fibrinogen-fibrinogen derived methods) may be an help in finding diabetic patients with clinical complications. To cite this abstract use the following format: Journal of Thrombosis and Haemostasis 2003; 1 Supplement 1 July: abstract number

http://www.biomedexperts.com/Abstract.bme/15843224/Interferences_in_coagulation_tests--evaluation_of_the_570-nm_method_on_the_Dade_Behring_BCS_analyser

2005: Junker Ralf; Käse Margit; Schulte Helmut; Bäumer Ruth; Langer Claus; Nowak-Göttl UlrikeInterferences in coagulation tests--evaluation of the 570-nm method on the Dade Behring BCS analyser.Clinical chemistry and laboratory medicine : CCLM / FESCC 2005;43(2):244-52.
The Dade Behring BCS is a coagulation analyser with optical reaction detection (standard 405 nm). The present study was conducted to evaluate measurement at 570 nm for analyses in interfering plasma samples. Prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen and D-dimer in normal (n=50), lipaemic (n=60), icteric (n=113), and haemolytic (n=58) samples were measured at 405 and 570 nm. As they are unaffected by the optical properties of the sample, the mechanical STAcompact analyser (Roche Diagnostics) and an ELISA technique were defined as the "comparison" methods. The percentage of valid PT results using the 570-nm method varied from 54% (lipaemic samples) to 97% (haemolytic samples). Valid aPTT measurements were found in 67% (lipaemic samples) up to 93% (icteric samples) of samples. Fibrinogen measurement revealed valid results in 58% (lipaemic samples) to 100% (haemolytic samples) of samples. The number of valid D-dimer results varied from 28% (lipaemic material) up to 100% (haemolytic material). Significant inter-method differences were found: aPTT in lipaemic (BCS 405 vs. 570 nm) and icteric samples (STAcompact vs. BCS 405 and 570 nm); fibrinogen in lipaemic (BCS 405 vs. 570 nm), icteric (BCS 405 vs. 570 nm; STAcompact vs. BCS 570 nm) and haemolytic samples (STAcompact vs. BCS 405 and 570 nm). Differences between the BCS 570-nm and the STAcompact methods were in most cases low and less pronounced than between the BCS 570- and 405-nm methods, making the BCS 570-nm method an alternative to measurement at 405 nm. Limitations have to be taken into account regarding lipaemic plasma.

2009-01-08T06:55:00.000-08:00

ALFRED
The ALlele FREquency Database
A resource of gene frequency data on human populations supported by the U. S. National Science Foundation.

Comparing multiple proportions: The Marascuillo procedure

2008-11-21T01:37:00.000-08:00

Comparing multiple proportions: The Marascuillo procedure

from NIST Handbook. includes syntax for calculation

BIOS nice overview of proportions / basics - equivalence of Pearson chi-square test and z-test

Macro from Minitab

This macro performs a multiple comparisons test on proportion data using # Tukey's honest significant difference test.

statistics for lawyers

google books

http://books.google.com/books?id=_bR9Q-EERlIC&pg=PA200&lpg=PA200&dq=comparing+multiple+proportions&source=bl&ots=PTb87Wa-gr&sig=PuEEGFcVwPlqSnhLUF6zXoXJ5p0&hl=en&sa=X&oi=book_result&resnum=5&ct=result#PPA201,M1

2008-11-10T05:04:00.001-08:00

lognormal distribution - on different methods of calculation of confidence intervals

http://epa.gov/esd/tsc/images/256cmb04lognorm.pdf

SEQUENCING low price, individual genome

2008-10-07T05:26:00.000-07:00

Low-Price Mapping SEQUENCING

companies developing/offering genome sequencing

- COMPLETE GENOMICS - 5000 $ /Reid, Radoje Drmanac
- applied biosystems
- Knome - cca 20 customers
- cf Systems Biology Institute as customer for complete genomics

datamining

2008-09-20T15:29:00.000-07:00

datamining in genetic/genomic research

finland Helsinki
DM in LD mapping ... haplotype association etc. PDF

PUBLICATIONS BY HANNU TOIVONEN, UNI helsinki

antivirus

2008-09-19T04:15:00.000-07:00

TROJAN DOWNLOADER WIN32/AGENT

http://www.f-secure.com/v-descs/trojan-downloader_w32_agent_brk.shtml

geektogo

http://www.geekstogo.com/forum/How-to-remove-trojan-win32-agent-akk-t179227.html

datamining intro

2008-09-18T15:15:00.000-07:00

datamining course materials from Australian national Uni,
- same as links below.
COURSE SLIDES -FROM slideshare.com

by prof Lanzi, some slides look identical to slides provided by ANU

- but generally looks good, COMPREHENSIBLE .....

DATAMINING, UNSUPERVISED RECORD LINKAGE.

Markus Hegland , australia

CHRISTEN
DATAMINING. CHALLENGES, MODELS, METHODS AND ALGORITHMS
year 2003
intro -- mainly from the standpoint of computation science.. algorithms
--
progream - FEBRL year 2008
Febrl - A Freely Available Record Linkage System with a Graphical User Interface Peter Christen Proceedings of the Australasian Workshop on Health Data and Knowledge Management (HDKM), Wollongong, January 2008.

- DISTANCE - EUCLIDEAN, PYTHAGOREAN ETC WOLFRAM MATH

ASSOCIATION RULES

- Support, confidence

Support gives total number of transaction of any particular item are occurring in datasets while confidence gives strength of a data in a dataset, we can say support is probability of A and B while confidence is conditional probability. Association rule based on these two characteristics.

-short intro

c-statistic

2008-09-15T07:28:00.000-07:00

____?????? I would like to know whether we can calculate C-statistic using SPSS >> 13.

> If by the "c-statisitc" you are referring to the measure of the > discriminative power of the logistic equation, you can calculate it by > saving the predictive probabilities from the logistic regression > analysis and running a ROC curve with the preditive probabilities as > the "test variable." The c-statistic is the area under the curve > value.

HTH

In R/S-Plus you can just use the lrm function in the Design package or:

mean.rank <- mean(rank(x)[y == 1]) c.index <- (mean.rank - (n1 + 1)/2)/(n - n1)
(where n1 is the number of observations with y=1)
or use the somers2 function in the Hmisc package.

Frank Harrell

statistics general

2008-09-09T01:15:00.000-07:00

Q&A by Seaman /course in psychology/

Newsom Portland UNI - handouts to course , SPSS examples

STATNOTES - WEBLECTURES. brief, explanatory, with formulas and examples of both manual calculation of basic tests and examples in SPSS.

semipartial correlation coefficient = Rsq change,,,,, semipartial = part correlation

structural equation modelling BASICS - Newsom handout

BTB - CHISQUARED

Dr Newsom has nice disclaimer on his page : "DISCLAIMER: I am not always right."

2008-09-07T05:56:00.000-07:00

sequencing the human genome

by Venter

cf dinococcus radiodurans -

genetics statistics microarray spss

2008-09-06T02:41:00.000-07:00

Genovese

tutorial on false discovery rate - looks comprehensible

//also see the article by authors of the method FDR /method for controlling multiple comparison problem / benjamini, hochberg from 1995

Step-by-Step Tutorial for analyzing Affymetrix expression microarraysin the R statistical environment: HELPWITHSCHOOL.COM

SPSS tutorials at texas ..

latex /superscripts/

SPSS macro basics at Raynald

SPSS datenmanagement mit SPSS googlebooks

gene set enrichment analysis editorial

random forests, self organizing maps etc.

Rodenburg

A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes

A Bayesian Measure of the Probability of False Discovery in Genetic Epidemiology Studies
Jon Wakefield*

PLoS computational biology

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor
Michał J. Okoniewski, Crispin J. Miller *

SPSS statistics resources

2008-09-03T02:05:00.000-07:00

flash/audiovisual tutorials with screenshots and narrated.

wide range of topics, including advanced ones like nonlinear, segmented, robust regression,

Box-Cox transformation, contour, surface plotting and much more....

*****************Uni TEXAS

2008-09-02T05:44:00.001-07:00

enrichment analysis - combining different sources of information

eg. gene set enrichment analysis

cf SW package GSEAP

problems SPSS/automation

2008-08-31T01:24:00.000-07:00

using SPSS OMS in split file mode. how to add labels/subtypes to create file with tables from all subgroups of splitting variable.

macro - cf learn - check german site

repeated measures ANOVA, SPSS

2008-08-30T11:45:00.000-07:00

RM ANOVA in SPSS from UCLA site

CRP cutoffs

2008-08-30T08:42:00.000-07:00

review CRP in clinical practice on Medscape by Musunuru 08/2008

Laaksonen 2005 - C-reactive protein in the prediction of cardiovascular and overall mortality in middle-aged men: a population-based cohort study

power and sample size programs

2008-08-27T06:48:00.000-07:00

Biostatistics Uni UCSF
list of statistical programs for different types of analyses - extensive

on estimation of power/ss for logistic regression in stata from UCLA

site - but rather simple calculations //by eugene demidenko //cf author of recent book on Mixed models

site2 - logistic regression with covariate with measurement ERROR, generalized linear models etc - ALSO GIVES PLOTS OF POWER, OR, SAMPLE SIZE

logistic regression

2008-08-27T04:58:00.000-07:00

dr Friel

Prof. Moosbrugger Uni Frankfurt /German
http://user.uni-frankfurt.de/~moosbrug/lehre/kap0506/Logistische_Regression.ppt

maths algebra BtB

2008-08-27T01:30:00.000-07:00

logarithms

some basic algebra

reader genetics

2008-08-26T06:05:00.000-07:00

Diabgen
Finland, Askenazi Jews, Pomerania Germans, English

rare SNP - value Gorlov 2007

power analysis for GWAS KLEIN 2008

exocrine pancreas reprogramming into betacells zhou 2008

ONLINE LEARNING

2008-08-26T01:48:00.000-07:00

videolectures - biology, genetics, bioinformatics
eg.
http://videolectures.net/msht07_omont_gbba/

COMMENT: browsed videolectures.net yester and tried to watch cca 3 lectures on bioinformatics but the level of presentation was rather mediocre. topics interesting, but presented by some phd students in an uninteresting , hard-to-follow way.
but there is much more stuff, maybe i just didnt get representative sample, so hope to find something interesting.

OTHER SOURCE OF LECTURES/courses FROM MIT
opensource lectures from massachussets institute of technology.

Quantile regression

2008-08-18T09:11:00.000-07:00

QUANTILE REGRESSION
BY ROGER KOENKER - GOOGLE BOOKS - ADVANCED MATHS
http://books.google.com/books?
id=Xi_dTAeAmGcC&pg=PA248&lpg=PA248&dq=quantile+regression+visualisation&source=web&ots=7JodXzWE8k&sig=0VWO5PTpFiAj7LaoARk3KkY8gok&hl=en&sa=X&oi=book_result&resnum=3&ct=result#PPA22,M1

2008-08-18T04:32:00.000-07:00

REGRESSION ANOVA MODEL SELECTION

R_SQUARED preferably adjusted
F test
Mallow's C criterion

www-stat.stanford.edu/~jtaylo/courses/stats203/notes/selection.pdf by Jon Taylor

Larsen Stat course http://statmaster.sdu.dk/courses/st111/module08/index.html

Multiple regression -ppt. inc forward/backward/stepwise/best-subset regression, some maths

REGRESSION AND ANOVA TUTORIAL

2008-08-18T01:12:00.001-07:00

NICE LIST OF LECTURES ON
REGRESSION AND ANOVA BY Dr Pia Veldt Larsen, Uni of Southern Denmark, Odense
- including regression model selection, residual analysis, factor analysis, logistic regression, and topics like transformation of variables etc.

statistics lectures, python, spss, R

2008-08-06T00:27:00.000-07:00

a FANTASTIC COLLECTION of lectures on statistics - from basic concepts to advanced topics such as nonlinear regression. with examples.
- refers mainly to SPSS software, but this is marginal. MAINLY the mechanics behind the different tests is explained. VERY INSIGHTFUL.
dr FRIEL

******
seems like INTRO / TUTORIAL on the following topics.

ON PYTHON AND SPSS

on R - the open source statistical program "R"

weighted least square regression

2008-04-29T00:06:00.000-07:00

A technique for correcting the problem of heteroskedasticity by log-likelihood estimation of a weight that adjusts the errors of prediction

if some assumptions of ordinarly least square OLS regression do not hold.
.... in case of heteroscedasticity
.....unequal precision/reliability of datapoints

1. san Houston Uni - Weighted least squares regression XXX
http://www.shsu.edu/~icc_cmf/cj_789/weightedLeastSquares2.doc
- very good and detailed review of the technique, from the description of situations when to use WLS /ie if violation of homoscedasticity/ to detailed and very clear examples how to perform it /mainly applies to SPSS, the output is provided/.
- discusses both approaches on calculating weights 1/residualising the response variable 2/log-likelihood estimation of weights
- includes some basic mathematics, mostly well comprehensible college-level, formulas perfectly support the statements in text
/dr Charles M. Friel - author of this text provides lecture notes to a wide selection of statistical topics, comparable to Garson's Statnotes, in some topic I found dr Friel's explanations more poignant.
http://www.shsu.edu/~icc_cmf/directory.htm

2. statnotes - garson -including exemplification on SPSS ooutput - insightful, but not much regarding the mechanics of weight estimation / but maybe not so important/.

3. NIST Handbook - nice figures, comparison of WLS with alternative of nonlinear transformation of response and predictor variables.

2008-04-11T03:48:00.000-07:00

relationship between

median, mean, mode

in skewed distributions

violations in discrete distributions and multimodal continuous ADVANCED, but accessible

by Hippel 2005 , journal of statistical education

transformations

2008-04-11T01:48:00.000-07:00

Transformations

Statnotes - transformations - as part of testing assumptions, by Garson
- very nice, some pictures

Dallal's example of transformation in linear REGRESSION
RULE of THUMB: first transform the response variable y to correct heteroscedasticity (heterogeneity of variance) than apply transformation to predictiors to achieve linear relationship (bivariate scatterplot)

similar recommendations by NIST
Transformations:
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

NIST handbook of statistics
http://www.itl.nist.gov/div898/handbook/index.htm

from STATNOTES: To correct left (negative) skew, first subtract all values from the highest value plus 1, then apply square root, inverse, or logarithmic transforms.

Journal

chass

journal of statistical teaching and education ???

2 factor anova

2008-03-29T17:31:00.000-07:00

from Dallals page Little Handbook of Statistical Practice

dairy farmer wished to determine which type of feed will produce the greatest yield of milk. From the research literature she is able to determine the mean milk output for each of the breeds she owns for each type of feed she is considering. As a practical matter, she can use only one type of feed for her herd.
Since she can use only one type of feed, she wants the one that will produce the greatest yield from her herd. She wants the feed type that produces the greatest yield when averaged over all breeds, even if it means using a feed that is not optimal for a particular breed. (In fact, it is easy to construct examples where the feed-type that is best on average is not the best for any breed!) The dairy farmer is interested in what the main effects have to say even in the presence of the interaction. She wants to compare
where the means are obtained by averaging over breed.
For the sake of rigor, it is worth remarking that this assumes the herd is composed of equal numbers of each breed. Otherwise, the feed-types would be compared through weighted averages with weights determined by the composition of the herd. For example, suppose feed A is splendid for Jerseys but mundane for Holsteins while feed B is splendid for Holsteins but mundane for Jerseys. Finally, let feed C be pretty good for both. In a mixed herd, feed C would be the feed of choice. If the composition of the herd were to become predominantly Jerseys, A might be the feed of choice with the gains in the Jerseys more than offsetting the losses in the Holsteins. A similar argument applies to feed B and a herd that is predominantly Holsteins.

Linar mixed models - resources

2008-03-04T16:10:00.000-08:00

Linar mixed models - resources

West, Galecki: Practical Approach

Linear Mixed Models: A Practical Guide Using Statistical Software

http://books.google.com/books?id=LSJ__7lDSdgC&printsec=frontcover&dq=west+galecki&ei=nPzOR7f0OJy8zATGpqmwBQ&sig=rI8DjvFAgy8W-5lcgbZX0WZTiXY
book-accompanying site with datasets, code, errata etc
http://www-personal.umich.edu/~bwest/almmussp.html

books google: Designing Experiments and Analyzing Data....
http://books.google.com/books?id=h-bMhmQMifsC&printsec=frontcover&dq=designing+experiments+and+analyzing+data&ei=pxfQR6mWHJPAzATw04iwBQ&sig=DlC1utBSuL1magJSjkdDxa-_-xw#PRA2-PA145,M1
- provides explanation of both ANOVA based mixed models with univariate and multivariate approach, as well as linear mixed models in the frame of multilevels modeling (chapters ,,,,)
- uses some mathematics, but in aN understandable form.

LIST of from site dedicated to HIERARCHICAL modeling
http://www.hlm-online.com/books/

multilevel data analysis - from basics - WEBCAST by Leroux
uwtv.org Multilevel data analysis

www.geocities.com/joophox/publist/whenwhy.pdf

Gelman

Data Analysis Using Regression and Multilevel/Hierarchical Models

Eugen Demidenko LMM: Theory and Application

MULTILEVEL MODELING - SOFTWARE
http://www.cmm.bristol.ac.uk/learning-training/multilevel-m-software/index.shtml

MM and R
http://www.cmm.bristol.ac.uk/learning-training/multilevel-m-software/r.shtml
package lme (Pinheiro, Bates 2000)
more recent version - lmer, lme4 (2005)
www.r-project.org/doc/Rnews/Rnews_2005-1.pdf

for Splus, R by Fox (2002)
cran.r-project.org/doc/contrib/Fox-Companion/appendix-mixed-models.pdf

LINEAR MIXED MODELS
http://www2.chass.ncsu.edu/garson/pa765/multilevel.htm
no mathematical formulas
mainly refers to SPSS, but can can be useful as introduction for any platform

Hubbard Alan longitudinal data analysis
marginal models, generalized estimating equations GEE, with different link functions - Poisson regression etc.
provides lecture notes, and chapters from his textbook on the analysis of longitudinal data (quite readable, but at moments requires to think about vectors, matrix albebra etc., last chapter on Mixed models is not (yet?) available online), includes examples of code for STATA, SAS.

www.nyu.edu/its/socsci/Docs/SPSSMixed.ppt
comparison of mixed models with GLM - some formulas, many PRACTICAL points

www.spss.ch/upload/1107355943_LinearMixedEffectsModelling.pdf

www.spss.ch/upload/1126184451_Linear%20Mixed%20Effects%20Modeling%20in%20SPSS.pdf

gsic.syr.edu/manuals/spss/SPSS%20Advanced%20Models%2015.0.pdf

longitudinal data analysis - mixed models,

COURSES
ONLINE -
statistics.com - Galecki see above - also author of a textbook
www.statistics.com/ourcourses/mixedmodels/
also check - http://www.hlm-online.com/books/

http://www.csc.fi/english/csc/courses/archive/GLM2008
september 2008 - helsinki - Mixed models in R

MAXIMUM LIKELIHOOD ESTIMATION
explained - BGIM - Purcell
http://statgen.iop.kcl.ac.uk/bgim/mle/sslike_1.html

http://tigger.uic.edu/~hedeker/ml.html
SAS, SPSS

PPT
blog.case.edu/jjw17/2006/04/27/ZyzanskiSeminar4bPowerpoint.ppt

SURVIVAL mixed models for survival analysis
doi.wiley.com/10.1002/bimj.4710390102
jas.fass.org/cgi/reprint/77/E-Suppl_2/147.pdf
http://www.ingentaconnect.com/content/bpl/biom/2001/00000057/00000001/art00012
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V8V-4KFV26C-1&_user=949847&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049130&_version=1&_urlVersion=0&_userid=949847&md5=8f89a4cc66b9fe62715703c0323305f0
http://www.wiwi.uni-bielefeld.de/~kauermann/survival/kauermann.pdf
http://links.jstor.org/sici?sici=0006-341X(200103)57%3A1%3C96%3AMMFSAW%3E2.0.CO%3B2-M

generalized linear model

online courses
XXXXXXX generalized - for quantitative, categorical, binary, count data XXXXXXXXXXXXX
http://genetics.agrsci.dk/statistics/courses/phd07/
in R

EXCEL MACRO resources

2008-02-04T07:12:00.000-08:00

links to some fora dealing with macros/VBA script for different tasks

eg hiding row/column depending on value in a cell

solution from allexperts.com

thread from ozgrid.com

SPSS resources, tutorials

2008-02-03T02:24:00.000-08:00

uni koeln - references

uni maastricht - some basic tutorials - as html, doc or pdf

SPSS automation OMS

2008-02-01T05:35:00.000-08:00

from SPSS ARCHIVE
Correlation output using OMS

OMS COMMAND OUPUT XML SYNTAX

UCLA SPSS OMS TO SPSS FILE
UNI MANNHEIM STH WITH DDI ??? XML CONVERTER

http://db.zuma-mannheim.de/DDI/Workshop/2007-10-24/DDI%203%20Workshop/SPSS%20DDI%20Converter/Test/sample_setups.txt

http://bib.kuleuven.be/ebib/data/handleidingen/spss_programming_and_data_management.pdf

OMS p309 data management levesQUE

SPSS XML DDI   DDI DATA DOCUMENTATION INITIATIVE

http://xml.coverpages.org/xslSoftware.html  2004 CF COCOON,

SPSS tutorials GERMAN

2008-02-01T04:51:00.000-08:00

NICE TUTORIALS IN FORM OF FLASH
BY HANS GRUENER, FREIE UNI BERLIN
RECENT

ON STATISTIC PROCEDURES, INTRO IN SYNTAX, SCRIPT, MACRO.

SPSS v12.

NICE, cave ö german

webinars

2008-01-25T03:47:00.001-08:00

http://www.beamyourscreen.com/EU/Welcome.aspx
beamyourscreen

SPSS for dummies

2008-01-25T01:30:00.000-08:00

http://media.wiley.com/product_data/excerpt/48/04701134/0470113448.pdf

SPSS for dummies - 1st chapter- sample
by griffith

includes chapters on command syntax, Python , and VBS scripting.

python textbook

2008-01-24T14:05:00.000-08:00

learning to progam PYTHON ale aj o VBScript a JavaScript by alan gauld
česky preklad !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
looks interesting, readable.

update How to Think Like a (Python) Programmer 2007
http://www.greenteapress.com/thinkpython/thinkPP.pdf
the update of the following book. ... by downey
How to Think Like a Computer Scientist 2002
Learning with Python
Allen Downey
Jerey Elkner
Chris Meyers

baldwin HTML - Python

about medical profession

2007-12-11T15:32:00.000-08:00

stop pagin me

nice articles

2007-11-28T10:45:00.000-08:00

population-based case-control teratologic study of oral erythromycin treatment during pregnancy
hungarian authors, nice language. methods.

gwas, framingham

2007-11-28T07:46:00.000-08:00

gwas for subclinical AS (IMT, CAC, AAI) - 100K, no genome wide significance

cf its related.
- echocardiography measurements, brachial endothelial function, stress ecgňň
- biomarkers
- hemostatic markers

matching

2007-11-28T07:34:00.000-08:00

1. Q: to match or not to match?
A: it depends - what study design?
a) advantages
b) disadvantages

2. how to match - types of matching
a) frequency matching
b) individual

in case-control studies - Does the ratio case vs control 1:n matter? the more the better?

overmatching - cf twin studies?

terms:
counter-matching - *********counter-matching Langholz 2001, 2005
flexible matching
optimal ?
propensity score matching

matching in genetic association studies
- aim - to avoid population stratification ???
genomic control
admixture

blogtips

2007-11-28T07:17:00.001-08:00

1. to include relevance of the link, type a number of asterisks (****) immediately in front of the link .
e.g. *********counter-matching Langholz 2001, 2005

http://kucej.blog.sme.sk/

statistics elementar courses

2007-11-28T04:30:00.000-08:00

EPBI 431 - STATISTICAL METHODS IN BIOLOGICAL & MEDICAL SCIENCES I
ppt presentations of basic concepts

genetic epidemiology

2007-11-28T04:23:00.000-08:00

genetic epidemiology , Khoury 1997 , book,

statistics in HLA epidemiology DORAK !!!!!!!!

cf aj recent scientific statement of AHA

genetic association, population substructure, admixture

2007-11-28T02:36:00.000-08:00

The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases
A Geert Heidema1,4 , Jolanda MA Boer1 , Nico Nagelkerke2 , Edwin CM Mariman3 , Daphne L van der A1 and Edith JM Feskens1,4

Ethnicity, Ancestry, and Race in Molecular Epidemiologic Research
*
Genetic structure in four West African population groups
**
Genetic Admixture among Hispanics and Candidate Gene Polymorphisms: Potential for Confounding in a Breast Cancer Study?
**

nih grants, gwa
*
genetics 2006
A General Population-Genetic Model for the Production by Population Structure of Spurious Genotype–Phenotype Associations in Discrete, Admixed or Spatially Distributed Populations
*
bertram JCI 2005
The genetic epidemiology of neurodegenerative disease
*
genetic epidemiology - respiratory diseases - nice comments (from Villejuif, Paris)
*
gen epid - psychiatry - nice remarks (2000)
*
2005 Markus, Dichgans
Genetic Association Studies in Stroke
Methodological Issues and Proposed Standard Criteria
cdc
Clinical Application of Genetic Risk Assessment Strategies for Coronary Artery Disease: Genotypes, Phenotypes, and Family History

*
genetic approaches to CAD
inc. multistage design

*
artificial intelligence chapter 1

Family-Based versus Unrelated Case-Control Designs for Genetic Associations
*
1983
GUIDELINES FOR THE STUDY OF GENETIC EFFECTS IN HUMAN POPULATIONS
inchem, WHO

* 2006
International Conference on Environmental Epidemiology & Exposure
*

software, genetic association studies

2007-11-22T08:32:00.000-08:00

PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Carlo significance testing.

observational studies, reporting

2007-11-22T08:19:00.000-08:00

http://www.strobe-statement.org/.

Strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies.

cf article in BMJ

interpretation of observational studies BMJ 1994

case control matching, genetic association studies

2007-11-22T06:33:00.001-08:00

role of matching in epidemiologic studies pdf

inverse sampling Keogh 2007 IJE http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxm019v1

Matching BMJ Stat notes - Bland, Altman 1994
and letter

optimal matching software - stat packages SAS, R (bipartite)

Journal of Statistical Software by Sekon - 47pp - 2007

Goldstein , Andrieu 1999 on detection of interaction GE - discusses COUNTERMATCHING method

Flexible Matching Strategies to Increase Power and Efficiency to Detect and Estimate Gene-Environment Interactions in Case-Control Studies.
Original Contributions American Journal of Epidemiology. 155(7):593-602, April 1, 2002.Sturmer, Til 1,2; Brenner, Hermann 1,2
Abstract: Lack of power is a pertinent problem in many case-control studies of gene-environment interactions. The authors recently introduced the concept of flexible matching strategies with varying proportions of a matching factor among selected controls (degree of matching) to increase the power and efficiency of case-control studies. In this study, they extended the concept of flexible matching strategies to the field of gene-environment interactions. They assessed the power and efficiency of such studies to detect and estimate gene-environment interactions under a variety of assumptions regarding the prevalence and effects of the environmental exposure and the genetic susceptibility as well as their association in the population. For each set of parameters, 10,000 case-control studies were simulated using varying degrees of matching. Traditional frequency matching increased the power and precision in most scenarios, but even greater gains were often obtained by increasing the prevalence of the environmental exposure in controls above the one in cases. The authors concluded that flexible matching strategies can increase the power and efficiency of case-control studies to detect and estimate gene-environment interactions compared with traditional frequency matching and therefore might help to alleviate the notorious lack of power of these studies in specific situations.
Flexible Matching in Case-Control Studies of Gene-Environment Interactions
2004 AJE, Saunders, Barrett

Multivariate and Propensity Score Matching
Software with Automated Balance Optimization:
The Matching package for R

reducing selection bias by propensity score matching (PPT) Bo Lu 2007
in SAS - MACRO

matching software" in R - matchbalance, match, genmatch

SPSS - XXXXX

SPSS - propensity score macro

matching for ethnicity using a panel of SNPs (pdf)

An Introduction to Matching and its Application using SAS®

The use and misuse of matching in case-control studies: the example of PCOS

Fertil Steril 2007

part of paper on "degree of matching and gain in power and efficiency of case control studies" in Epidemiology 2001

(terms frequency matching, ...)

cf counter matching - (counterintuitive matching) to increase informative pairs

example - countermatching on radiation exposure from IJE 2004

advanced ??

file:///C:/Documents%20and%20Settings/Javorsky/Local%20Settings/Temporary%20Internet%20Files/Content.IE5/K1UJG9UN/256,1,Reducing Selection Bias via Propensity Score Approach

optimal case control multivariate matching

---------------------------------------------

HILDA australian data - social survey

regular expressions resources

2007-11-22T06:28:00.000-08:00

library of regexps

some intro McCook 2003

Finnish !

2007-10-31T11:46:00.000-07:00

to your attention
starter Helsinki uni (yliopisto)

morphological analyzer (parser) from xerox.
cf for "Minun mieheni nimi on Timo." (meaning Mon mari s’appelle Timo.) gives:
Result of Finnish Morphological Analysis :
Minun minä +PRO+GEN
mieheni mies +N+PL+NOM+PSG+PSF1
mieheni mies +N+SG+GEN+PSG+PSF1
mieheni mies +N+SG+NOM+PSG+PSF1
nimi nimi +N+SG+NOM
on olla +V+ACT+IND+PR+SG+PER3
Timo. Timo. +?

CONJUGATOR from verbix

at verbix.com there is also a list of 10000 most common used Finnish words

statistics resources

2007-10-31T08:02:00.000-07:00

from DISCOVER ô long list of resources on regression etc etc .........

comparison of statistical packages Stata, SAS, SPSS,
technical reports at UCLA 2007

from australian page for statistics course/exam in radiation oncology training (PDF)

statistics page by Dallal from Tufts - nice basic concepts, up to regression analysis (not so good logistic reg)

BUT involves treatise on estimation of CI for transformed data (eg log) !!!!!!!

LernSTATS - german/english - sociology-psychology - java examples

- up to factor analysis, some examples intuitive

lisrel online kurs - SEM - structural equation modelling - german FU Berlin

kuopio PhD, finnish resources

2007-10-24T12:25:00.000-07:00

RESOURCES on FINNISH language

blog on fremdsprachen und neue medien (podcast etc) by german teacher (unfortunately no link to finnish)

On Finland and Finnish

suomi-info.de - XXX very nice site in german, includes links to Finnish culture, short course on Finnish language and resources (eg how to subscribe to YLE podcast)

finnish

finnish grammar

- book Finnish: Essential Grammar, by Karlsson /1st ed 1999, 2nd edition end Nov 2007)

sites - to be used as complementary resources for novices XXX

0. a very short finnish grammar - nice brief "one webpage" overview

1. Kimberli Mäkäräinen

2. Panu Mäkinen - English, german, structured, but some grammar concepts just given as bulky examples without explanation (eg. consonant gradation)

3. ressources pour le finnois - from forum at Inalco - dept for languages of northern and eastern europe .....

http://virtual.finland.fi/netcomm/news/showarticle.asp?intNWSAID=25831
http://www.cs.tut.fi/~jkorpela/Finnish.html

absolute starter on finnish - SUPERB - with embeded audio.:.
http://donnerwetter.kielikeskus.helsinki.fi/FinnishForForeigners/parts-index.htm
http://donnerwetter.kielikeskus.helsinki.fi/FinnishForForeigners/parts-index.htm
quiz - finnish english vocabulary

DICTIONARY + resources XXXXX

finnish in finnish

YLE radio, tv podcast !!!!XXXX how to subscribe see - suomi-info.de

maybe some resources can be found here

PhD in Kuopio

http://www.uku.fi/laake/english/forms.shtml http://www.uku.fi/laake/english/studies.shtml http://www.uku.fi/intl/english/prospective/applying.shtml#PG IMPIT cf International Master´s Program in Information Technology research at Dept of Computer science and applied mathematics Structured Documents

databases, intro, relational, Access tutorial

2007-10-24T09:35:00.000-07:00

some INTRO resources on databases (database management systems, DMBS) especially the so called relational databases
- tutorial-like resources

1. databasics from scratch - instructional, very understandable (at geekgirls.com ....???)

2. types of databases -
flat spreadsheet / hierarchical / relational / object oriented
- a brief (minimal) theoretical intro with examples of structure and questions/queries - also (Funnel 2007, McGill Uni)

3. intro to Access - (basic relational db available as part of MS Office)
very instructional TUTORIAL - really click-by-click intro into designing creating, viewing, querying a relational database. (holowczak from Baruch College CUNY) with multiple screenshots.

4. designing and creating relational database - course/tutorial - looks comprehensible with multiple figures to describe problems with designing db, however some links broken (Newcastle 2004)
also some useful guides on software by administrators at Newcastle
eg access, excel, word, spss.
check using ACCESS and SPSS

5. Dilip´s brief intro to relationdal db (1998), schemes, screenshots + some syntax.

perl, intro, resources

2007-10-23T11:03:00.000-07:00

perl
- program - originally developed to transform various dataformats
- useful for data manipulation
- esp. text manipulation by means of regular expressions
- web pages (amazon.com etc)
- cf data manipulation for Human Genome Project
-
- Bioperl - (manipulation and evaluation of genome sequence data)

can be downloaded free from activestate.com as ActivePerl

intro at perl.com, perl.org, where also a library with online books can be found
eg. beginning Perl by S. Cozens
at CPAN - official Perl site with comprehensive documentation-

intro text also here, helps to get first glimpse on the structure of perl + one gets acquainted with some terminology (variable types-scalar, array, hashes, references, subroutines, regular expressions), but not many "aha" feelings so far. however - nicely organized.

PERL INTRO + links to other INTROs and more
Broman´s page - reads very well

Perl code editors - syntax color coding, ....
FREE:
Perl Express - looks trustworthy - last update 2005?
Open Perl IDE looks like OptiPerl - from 2003+patch for Perl 5.8
Perl code editor - basic, webpage rather shabby

shareware
OPTIPERL intergrated environment - looks interesting
DZSoft Perl Editor

ER stress

2007-10-17T11:05:00.000-07:00

2007 - Ind J Med Res

ER stress and diabetes. Sundar Rajan

2006 - Science - Hotamisligil.

chemical chaperones reduce ER stress and restore glucose homeostatis in mouse model of T2DM

XXXX - 4-phenylbutyric acid, taurine-conjugated ursodeoxycholic acid

cf XXXXX treatment of ER stressss, cf cited bys

2006 - Phys Reviews
Marinciak S. Endoplasmic Reticulum Stress Signaling in Disease

2005 - JCI
Xu, Bailly-Maitre, Reed. Endoplasmic reticulum stress: cell life and death decisionsJ. Clin. Invest., Oct 2005; 115: 2656 - 2664.

2005 - JBC
Nakatami. Involvement of Endoplasmic Reticulum Stress in Insulin Resistance and Diabetes *

2002 - JCI
David Ron - Translational control in the endoplasmic reticulum stress response J. Clin. Invest., Nov 2002; 110: 1383 - 1388.

quantitative genetics veterinary

2007-10-17T11:03:00.000-07:00

quantitative genetics in veterinary medicine - a booklet

http://www.kursus.kvl.dk/shares/vetgen/_Popgen/genetics/genetik.htm

statistics genetics "a must see"

2007-09-22T08:42:00.000-07:00

http://www.dorak.info/genetics/notes05.html

European Genetics Foundation
http://www.charite.de/ch/medgen/eumedis/statistics05/genetic-epidemiology.html

article by Kruglyak, Nickerson on the effect of SNP frequency on the LD and a measure of frequency matched SNP correlation.

linear trend ordinal variables

2007-09-22T08:30:00.000-07:00

linear trend test for dichotomous(binary) with categorical-ordinal variables
e.g. linear trend of risk (OR) of some disease across genotypes

Cochran-Armitage - in SPSS can be done as - sort of - CROSSTABS - linear-by-linear association

more theory + statsdirect software

statistics resources

2007-09-22T08:27:00.000-07:00

statistics resources + accompanying SPSS syntax
as recommended by Marta Garcia-Granero

at www.nabble.com

The book: http://www.bmj.com/collections/statsbk/
The SPSS syntax: http://www.kingdouglasconsulting.com/SPSS/DiverseCultures/Marta/Code/BMJ%20-%20Stats%20Square%20One.txt

statistics resources

2007-09-05T13:08:00.000-07:00

XXXXXX
the well known series by dr Bland et ???? that appeared in BMJ
statistics at square one

XXXXXX
very instructive resource (maryland biology) by McDonald

measures of central tendency (location)

mean (arithmetic, geometric, harmonic)
median
mode

anova POST HOCS EG:

http://www.uwsp.edu/psych/cw/statmanual/posthocs.html

statistics resources, tutorials, SPSS, other

2007-08-31T14:27:00.000-07:00

resources on statistics
1. xxxxx - comprehensive at onlinetutorialsstatistics. ... as of 2000?

okstate.edu - also other tutorials
http://home.okstate.edu/homepages.nsf/toc/onlinetutorials

R resources

2007-08-31T13:38:00.000-07:00

graphics:

addictedtoR

intro - multiple tips: Using R for psychological research:

fora (pl. forum)

nabble seems nice
cf thread - regular expressions ..... "solution to my problems?"

ANOVA, permutation test, in R

2007-08-31T12:43:00.000-07:00

while searching for a code in R to run a permutation test on ANOVA (eg. genotype - continuous variable association, adaptation of p values etc.) I found the following resources valuable:

some resources on ANOVA calculation in R and permutation test when comparing multiple groups (more than two)

mrpp function in vegan package seems to be appropiate (as an alternative to permutation test and comparison of F-values), cf measures of distance (euclidian, delta etc.)
MRPP stands for
Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities

certainly a comprehensive resource on ANOVA in R is
Faraway´s: Practical Regression and Anova using R (pdf) 200+ pages

very nice intro in ANOVA 3pp (pdf)

site by the Dutch Guido W to accompany some textbook by neter (1996), but nevertheless seems informative/instructive

(((((((( what is this about?????))))))
voila: fast introduction to the concept of resampling, randomization (and permutation) tests, bootstrapping can be found on pages of David Howell. david also provides a free software, which is very easy to install, use and understand. However, it may not be used for publications, as the algorithms is not clear etc. Anyway, a very nice site and software.
check david howell´s site here.
other resource is the freely available book (pdf) of Simon´s book - e.g. on statistics.com

les examples utiles de code en R pour les analyses simples je trouvait sur la site de Christian Jost dans le cadre de ses courses
Données pour les TP du module 3L3B03M 'Traitement des données en biologie' (http://cognition.ups-tlse.fr/_christian/L2-BopeStat/index.html)

e.g. intro pdf

ANOVA ici XXXXXXXXXXXXXXXXX

aussi en Francais est le contribution de Mr Pallier
les exemples d´ ANOVA - (pdf)
montre les differentes designs d´ANOVA (one/two-way, factorial, repeated measures, nested, hierarchical etc)

forum francais (groupe d´utilisateur du logiciel R)

Just to repeat what is ANOVA about
and link to some other basic statistical concepts can be found on Stattrek.com

causality, complex genetic disease

2007-07-01T13:44:00.000-07:00

"Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. by Page GP et al, Am J Hum Gen 2003
back in 2003 was published nice overview of the causality concept of complex multifactorial polygenic diseases. author mentions Hill´s criteria for causality in epidemiological research, as well as those of Koch´s postulates, along with the review of causality concepts from the scientific to philosophical standpoint. Page discusses the common problem of causality vs association, and gives a step-by-step detailed treatise of what can be cause of a positive genetic association.

here you can read article in AJHG 2003

sample size, general, genetic association, SW

2007-07-01T09:14:00.000-07:00

discussion of/ and practical guide on sample size determination - in general
by Lenth, Effective sample size determination
Lenth is author of Java based software for sample size/ power estimation. it is very intuitive
classical web-based calculators of power and sample size for GENETIC ASSOCIATION studies are:
Purcell´s site:
Genetic power calculator

and Derek Gordon´s calculator, allowing researchers to take into account possible genotypic error and/or misclassification errror:

PAWE - Power for Association With Errors

also see Gordon´s article on factors affecting statistical power in the detection of genetic association which was published as part of the JCI review series on genetics of complex diseases.

primer of allelic association

2007-06-29T15:24:00.000-07:00

základy genetických asociačných štúdií - vysvetlené na príkladoch spred éry HUGO project.
includes TDT analysis and GE interactions, case-only designs (Khoury)

a primer of allelic association

interakcia, viacrozmerná lineárna regresia

2007-06-29T13:54:00.000-07:00

prehľad testovania interakcií v multivariatnom linearnom regresnom modeli.
formou častých otázok (FAQ - pýtate sa).

interakcia, MLR

interakcie gény, gén prostredie, epistáza, software MDR

2007-06-29T11:03:00.000-07:00

pre záujemcov o genetiku a interakcie medzi génmi, génmi a faktormi prostredia odporúčam blog Jasona Moore-a z Vanderbildtovej Uni. Jason je spoluautorom jednej z metód na testovanie interakcií medzi génmi (epistázy) ako aj príslušného softwéru - multifactor dimensionality reduction, MDR.
epistasis blog

Moore JH. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered. 2003;56(1-3):73-82. pubmed
There is increasing awareness that epistasis or gene-gene interaction plays a role in susceptibility to common human diseases. In this paper, we formulate a working hypothesis that epistasis is a ubiquitous component of the genetic architecture of common human diseases and that complex interactions are more important than the independent main effects of any one susceptibility gene. This working hypothesis is based on several bodies of evidence. First, the idea that epistasis is important is not new. In fact, the recognition that deviations from Mendelian ratios are due to interactions between genes has been around for nearly 100 years. Second, the ubiquity of biomolecular interactions in gene regulation and biochemical and metabolic systems suggest that relationship between DNA sequence variations and clinical endpoints is likely to involve gene-gene interactions. Third, positive results from studies of single polymorphisms typically do not replicate across independent samples. This is true for both linkage and association studies. Fourth, gene-gene interactions are commonly found when properly investigated. We review each of these points and then review an analytical strategy called multifactor dimensionality reduction for detecting epistasis. We end with ideas of how hypotheses about biological epistasis can be generated from statistical evidence using biochemical systems models. If this working hypothesis is true, it suggests that we need a research strategy for identifying common disease susceptibility genes that embraces, rather than ignores, the complexity of the genotype to phenotype relationship.

tu je odkaz na článok o metóde MDR
Hahn
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions.Bioinformatics. 2003 Feb 12;19(3):376-82.

v tomto článku nájdete prehľad používaných metód na štúdium interakcií predovšetkým medzi génmi.

Heidema
The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases.BMC Genet. 2006 Apr 21;7:23.