[BioC] LIMMA decideTests result zero from contrast matrix
alexg at ruggedtextile.com
Wed May 9 10:19:42 CEST 2012
On 09.05.2012 04:21, Ekta Jain wrote:
> Dear Jim,
> I did change things around when you pointed out for the first time.
> All I have been doing is
>> numGenes <- rownames(eset)
>> topTable(fit2, coef=1, adjust="BH", sort.by="B", number=numGenes)
>> results<-decideTests(fit2, method ="global", lfc =0)
> As you mention in your email that "by default decideTests() uses a BH
> adjusted p-value to filter genes" so am i not applying the same
> adjustment for both the toptable() and decideTests() here?
> This is what I am clueless about since I still get zero genes. I
> cannot seem to figure out how to not let decideTests use a BH adjust
> for p-value. For the sake of detail, the code worked fine for all my
> cell lines treated with CPI since the p-values were not as bad as the
> ones for treatment with DMSO.
> Thank you,
I think it is the difference in the default P value cutoffs for
topTable and decideTests that is confusing the issue. From the
Look at the default p.value cutoff - 0.05. Earlier in the thread you
said your adjusted P values were ~0.9, hence *nothing* will come through
the filter. The default for topTable is 1:
topTable(fit, coef=NULL, number=10, genelist=fit$genes,
sort.by="B", resort.by=NULL, p.value=1, lfc=0,
If you want to apply the filter to unadjusted P values the docs say
adjust.method: character string specifying p-value adjustment method.
Possible values are ‘"none"’, ‘"BH"’, ‘"fdr"’ (equivalent to
‘"BH"’), ‘"BY"’ and ‘"holm"’. See ‘p.adjust’ for details.
Though I'm not sure why you would want to do this.
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