[BioC] questions on results from mt.maxT (multtest)
P.D. Moerland
P.D.Moerland at amc.uva.nl
Mon Feb 14 17:35:45 CET 2005
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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