Alex Gutteridge <alexg at="" ...=""> writes: > > On 20.01.2012 05:11, Vladimir Zhurov wrote: > >> ... > > > > Dear Bioconductors, > > > > I am having the following problem which can be due to a > > misunderstanding, > > or an actual problem with topTable function in limma package. > > > > As far as I understand lfc and p filters should work together in > > filtering > > topTable results. Am I correct in this regard? > > > > If it is an intended situation then the problem is the following: > > when more > > than one contrasts is reported lfc filter does not affect the output. > > Which > > is shown in the sample R session below. > > > > I would appreciate you help. > > > > Regards. > > > > Vladimir. > > > > Hi Vladimir, > > I think the issue maybe that it is not clear (to me anyway!) what > result one would expect with a lfc filter on a table with multiple > contrasts. Should rows where all contrasts are above the cutoff be > reported? Or where any are? It doesn't seem to be explicit in the docs, > but my assumption is that to avoid confusion topTable ignores lfc= in > the case you describe. > > Perhaps decideTests() is what you are really looking for? You can then > index a topTable generated data.frame with the results of decideTests. > E.g (pseudo-code not tested!) > > tt = topTable(fit,p.value=1,number=Inf,sort.by="none") > dt = decideTests(fit,p.value=0.05,lfc=1) > > tt[dt[,1] != 0 & dt[,2] != 0 & dt[,3] !=0,] #Gives rows where all > contrasts pass filter (assuming 3 contrasts) > tt[dt[,1] != 0 | dt[,2] != 0 | dt[,3] !=0,] #Gives rows where any > contrast passes filter > Alex, Thank you for your input. I was considering decideTests but wanted to check whether there is something that can be done with topTable. I think that it would be nice at very least to explain intended behavior in more details in the manual for a case of multiple contrasts comparison. Anyway, I ended up with the following workaround (lets say lfc=1, p=0.05 and no adjustment of p value): tt.all<-topTable(fit.eb, sort.by="none", number=Inf, adjust.method="none") dt<-decideTests(fit.eb, lfc=1, p=0.05, adjust.method="none", method="separate") rs<-rowSums(abs(dt)) tt<-tt.all[rs >= 1,] # a single contrast above lfc will be sufficient One may think that you are done at this point. However, decideTests with method="separate" recapitulates topTable performed on individual contrasts. As a result there are extra probes which will be reported and will have p value above cut-off when topTable is done across multiple comparisons. They need to be further filtered out. tt.filt<-tt[tt$adj.P.Val < 0.05,] Regards. Vladimir.