[BioC] multtest problem...

[Sean Davis]

On Apr 29, 2005, at 5:58 AM, Dipl.-Ing. Johannes Rainer wrote:

> hi,
>
> i used the mt.teststat function from the package multtest and wonder 
> why the p values that the function calculates differ from those i get 
> using the wilcox.test or t.test function.
> i tried it with the golub data set (data(golub)) and 
> wilcox.test(x=golub[,golub.cl==0],y=golub[,golub.cl==1])
>
> returns a p-value = 0.8987
>
> while teststat<-mt.teststat(golub,golub.cl,test="wilcoxon")
>
> teststat[1] = 1.75419
>
> i thought that the mt.teststat funciton uses simple t tests or wilcox 
> test to calculate p values...
>

Looking at the help for mt.teststat (by typing help(mt.teststat)), you 
can see part way down:

Value:

      For 'mt.teststat', a vector of test statistics for each row
      (gene).

The test statistic is NOT a p-value.  You have to convert it to a 
p-value using some other function (usually something like pnorm, pt, 
etc).  Finally, you will need to apply mt.rawp2adjp to get corrected 
p-values.  I would suggest reading the mt.teststat vignette for more 
information and worked examples, including how to calculate p-values 
from mt.teststat output.

Hope this helps,
Sean