[BioC] Multiple testing correction for SimpleAffy t-tests

[James W. MacDonald]

Brian Lane wrote:
> Can anyone tell me if the t-tests generated by the SimpelAffy 
> pairwise.filter function which are applied to pairwise.comparison objects 
> have been corrected for multiple testing? If so which correction is applied 
> by default and are there any options?

First, a pedantic note; neither the t-test nor the t-statistic are 
adjusted for multiplicity. The only statistic that is commonly adjusted 
is the p-value.

However, it doesn't help that these functions use 'tt' to indicate the 
t-test p-value. I can see where you might have been lead astray.

Anyway, if you dig through the functions, you will see that the p-values 
are not adjusted. They come from either fastT() in the genefilter 
package, or t.test() (for paired comparisons) in base R's stats package.

HTH,

Jim


> 
> Regards,
> Dr. Brian Lane
> Northwest Institute for Bio-Health Informatics
> University of Liverpool
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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