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Hi Ingrid, I think the differences you observe in how your specify the number parameter in the topTable function. Try something like the following code: top <- topTable(fit2,coef=1, adjust="BH", sort.by="P", number=length(fit2$genes)) top <- top[top$adj.P.Val <0.01,] dim(top) and desTest <- decideTests(fit2, adjust.method="BH", p.value = 0.01) vennDiagram(desTest) gives you the same number of DE genes for a given contrast (notice that you have to specify contrasts or "coef", in topTable) If you want to use fold change cutoff of M>2, you can also specify this in: top <- topTable(fit2,coef=1, adjust="BH", sort.by="M", number=length(fit2$genes)) top <- top[top$M>2,] hope this helps, morten Ingrid H. G. ?stensen wrote: > Hi > > I am analyzing Affymetix data and have loaded the data, done gcrma, made the design matrix, lmFit, makeContrasts, contrasts.fit and eBayes. Now I would like to know which genes are differentially expressed and have a fold change >= +-2. > > I have used the following command to get an overview of the changing genes over all the contrasts: > > desTest <- decideTests(fitContr2, adjust.method=?BH?, p.value = 0.01) > > This is a great function! But how can I get more information about the genes: p-values etc? I have tried to use topTable > > tilFil <- topTable(fitContr2, coef = 1, number= 100, adjust.method = ?BH?) > > but it is hard to get the same genes from the two functions (topTable and decideTest), and it is hard to find a good cut of for the number of genes to include in the topTable function. > > Does any one have any suggestions? > > When I use topTable I get different parameters and I am trying to understand what the different parameters can tell me but I am still confused about M and log-odds. (And yes I have read a lot of documentation and books, but no one seems to agree/explain it good enough for me to understand) > > Regards, > Ingrid :-) > > > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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