[BioC] questions on results from mt.maxT (multtest)

[Straubhaar, Juerg]

Hi Wolfgang,

I don't quite understand what you mean by 'parametric test': the mt.maxT function has a parameter 'nonpara' which is set by default to 'n'. I assume a parametric test was performed.

Juerg


-----Original Message-----
From: Wolfgang Huber [mailto:huber at ebi.ac.uk]
Sent: Sun 2/13/2005 12:12 PM
To: Straubhaar, Juerg
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] questions on results from mt.maxT (multtest)
 
Hi Juerg,

the p-values from a permutation test are multiples of 1/(number of 
permutations). If you want p-values with more digits, you need to do a 
parametric test.

You say your exprs matrix has 6 colums, but in the call to mt.maxT you 
only have 5 classlabels. Wrong?

  Bw
   Wolfgang


Straubhaar, Juerg wrote:
> Im am using R version 2.0.1, multtest version 1.5.2.
> 
> Microarray experiment: wildtype tissue vs KO tissue; affy MOE430_2
> Experiments in triplicates.
> 
> ExprSet at exprs matrix has dimension: 45101 6
> 
> I used nonspecific filtering which reduces the number of genes to 1815 (exprSub)
> 
> I am using multtest to get a set of differentially expressed genes:
> 
> resT <-mt.maxT(exprSub at exprs, c(0,1,0,1,0))
> This runs 20 permutations (complete enumeration)
> 
> sort(resT$rawp) looks like this:
> 
> [1] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> [20] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> [39] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> ...
> [1711] 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9
> [1729] 0.9 0.9 0.9 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1747] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1765] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1783] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1801] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> 
> It looks like these p-values are rounded to one decimal digit. From these results none of the 1815  genes are differentially expressed between WT and KO, which is not quite believable. I would like to get p-values precise to several digits. Maybe there is something else I don't understand.
> 
> getOption('digits') 7
> 
> Thank you.
> 
> Juerg Straubhaar
> Umass Med
> 
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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