[BioC] SAM and qvalue

[Holger Schwender]

Hi Nicolas,

yes, the p-values in the summary are the raw p-values (in the latest versions of siggenes, they are also referred to as rawp and not p.value anymore). With SAM p-value in my last mail I have meant these raw p-values. There are no SAM adjusted p-values for individual genes. There is "only" the FDR as an error rate for a list of genes.

Best,
Holger


-------- Original-Nachricht --------
Datum: Tue, 07 Nov 2006 18:47:12 +0100
Von: Nicolas Servant <Nicolas.Servant at curie.fr>
An: Holger Schwender <holger.schw at gmx.de>
Betreff: Re: [BioC] SAM and qvalue

> Thanks for your answer.
> If the qvalues are computed as in the R package qvalue, I suppose that 
> the "p.values" column of the results represents the raw pvalues.
> So where can i found the pvalues adjusted by SAM ?
> Best,
> 
> Nicolas
> 
> Holger Schwender wrote:
> > Hi Nicolas,
> >
> > these differences are due to the differing calculation of the FDR and
> the q-value. The FDR is computed using the observed and expected d values
> that fall outside the interval (cutlow, cutup), whereas the q-values are
> computed as in the R package qvalue and based on the SAM p-value which uses
> symmetric thresholds, i.e., e.g., (-cutup, cutup). So it can and will happen
> that not all q-value estimates are smaller than the FDR value if, e.g.,
> |cutup|>|cutlow|.
> >
> > Best,
> > Holger
> >
> > -------- Original-Nachricht --------
> > Datum: Mon, 06 Nov 2006 16:38:23 +0100
> > Von: Nicolas Servant <Nicolas.Servant at curie.fr>
> > An: Bioconductor <bioconductor at stat.math.ethz.ch>
> > Betreff: [BioC] SAM and qvalue
> >
> >   
> >> Hi all,
> >>
> >> I have a question about SAM (siggenes) and its adjusted pvalues
> (qvalues).
> >> When i perform SAM on Golub data for a FDR threshold = 5%:
> >>
> >> FDR=5/100
> >> output<-sam(golub,golub.cl,rand=123,delta=seq(0.1,5,0.05))
> >> res.sum<-summary(output)
> >> sum.output <- res.sum at mat.fdr
> >> delta<-sum.output[sum.output[,"FDR"]<=FDR,][1,"Delta"]
> >> delta.sum<-summary(output,delta)
> >> ds.mat.sig <- delta.sum at mat.sig
> >>
> >> I found 894 significant genes.
> >>     Row   d.value      stdev      p.value      q.value    R.fold
> >> 1    829  8.165222 0.29582512 0.000000e+00 0.000000e+00 7.2771792
> >> 2   2124  7.964784 0.17786969 0.000000e+00 0.000000e+00 3.3953035
> >> 3   2600  6.102371 0.19112194 0.000000e+00 0.000000e+00 2.6686992
> >> ....
> >> 892  142 -1.689638 0.11912464 3.305801e-02 5.393673e-02 0.8178807
> >> 893  864 -1.689047 0.08528524 3.312029e-02 5.393673e-02 0.8312349
> >> 894  686 -1.689045 0.20350807 3.312029e-02 5.393673e-02 0.7272737
> >>
> >> For a FDR threshold, SAM use the Delta, the cutlow and the cutup values
> >> to find significant genes.
> >> How can we explain that the last genes of my list have a qvalue bigger 
> >> than 5% (my FDR threshold) ?
> >> I notice that their dstatistics are in the good range (cutlow-cutup),
> It 
> >> certainly explains why these genes are significants.
> >>
> >> Thanks for your help !
> >> Best Regards,
> >>
> >> Nicolas
> >>
> >> -- 
> >> Nicolas Servant
> >> Equipe Bioinformatique
> >> Institut Curie 
> >> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
> >>
> >> Email: Nicolas.Servant at curie.fr
> >> Tel: 01 53 10 70 55
> >> http://bioinfo.curie.fr/
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>     
> >
> > --
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > .
> >
> >   
> 
> 
> -- 
> Nicolas Servant
> Equipe Bioinformatique
> Institut Curie 
> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
> 
> Email: Nicolas.Servant at curie.fr
> Tel: 01 53 10 70 55
> http://bioinfo.curie.fr/

--