statistics resources

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

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

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very instructive resource (maryland biology) by McDonald

measures of central tendency (location)

1. mean (arithmetic, geometric, harmonic)
2. median
3. mode

anova POST HOCS EG:

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

statistics resources, tutorials, SPSS, other

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

graphics:

1. 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

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

"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

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.