[BioC] (stupid) question about wilcoxon test and finding interesting genes

[James W. MacDonald]

Dipl.-Ing. Johannes Rainer wrote:
> hi,
> i must excuse myself for my question, but i'm not really good in 
> statistics...
> 
> we have done affymetrix genechips with samples from patients before and 
> after treatment. until now i searched for genes that are influenced by 
> the treatment using M values but i wanted also to apply a statistical 
> test to get some proof that the genes i found are significant.
> 
> so i applied a wilcoxon paired test to the expression values (one test 
> per gene). my samples size is 13 (13 chips with samples before treatment 
> and 13 afterwards). i subtracted the values after treatment from those 
> before treatment (
> 
> p.vals <- apply((untreated-treated),MARGIN=1,wilcox.test) , untreated is 
> a matrix with 13 columns and 54000 rows (genes) and the same is 
> treated). according to the p values i got nearly every gene is 
> significant, also if the gene is not regulated.
> 
> so my question, do i have to correct the p values or was i totally wrong 
> with the assumption to get significant (and regulated) genes in this way?

You have to correct the p-values to account for the fact that you have 
done 54,000 simultaneous tests. See e.g., ?p.adjust

Jim


> 
> thanks
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109