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

[P.D. Moerland]

Hi Juerg,

what Wolfgang means is that in your case with six samples, three from
each class, you can only have (6 choose 3)= 20 permutations of the class
labels. That's why your p-values will always be multiples of 1/20. A
permutation test is not suitable with so few samples; you should use one
of the standard tests (t, Wilcoxon, limma's robust t) and then correct
for mulitple testing.

Best wishes,
Perry

----- Original Message -----
From: "Straubhaar, Juerg" <Juerg.Straubhaar at umassmed.edu>
Date: Monday, February 14, 2005 5:08 pm
Subject: RE: [BioC] questions on results from mt.maxT (multtest)

> 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
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> 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
> 
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