[BioC] multtest problem...

[Dipl.-Ing. Johannes Rainer]

:) thanks for the help

Quoting Sean Davis <sdavis2 at mail.nih.gov>:

>
> 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
>
>