[BioC] multtest problem...

[Wolfgang Huber]

Hi Jo,

your mail is not very clear about the distinction between test 
statistics and p-value, and perhaps this is where your confusion comes from?

There is no reason why the two numbers you state in your mail should be 
equal, they are different things.

Have a look as well at the function rowttests in the develop version of 
"genefilter", for a fast and userfriendly approach to doing t-tests for 
each row of an exprSet.

   Best
   Wolfgang




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...
> perhaps i am wrong with the class labels?
> 
> from the help i understood, that if i have two groups in my samples i 
> submit as classlabels for examples c(0,0,0,1,1,1) and this means that 
> the first 3 columns of my data correspond to group 0 and the other 3 to 
> group 1. is this correct?
> 
> thanks, jo
> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber