[Reposting from bioc-devel to bioconductor, where this mail should have gone to] Hi Jarod Mike overlooked one point in your question On 11/07/14 12:05, jarod_v6 at libero.it wrote: > If I interested in the genes that have a foldchange more than 0.5 and 2 I need > to use this comand is it right? DESeq2 reports al fold changes on a log2 scale. So your limits of 0.5 and 2 for unlogarithmized fold changes translate to -1 and +1 on the log2 scale (because 2^(-1)=0.5 and 2^1 = 1, with '^' meaning 'to the power of'). Also, the 'lfcThreshold' parameter wants an _absolute_ log fold change. Hence, you want: ddsNoPrior <- DESeq(ddHTSeq, betaPrior=FALSE) res <- results(ddsNoPrior, lfcThreshold=1, altHypothesis="greaterAbs") to get a list of all genes with an absolute log2 fold change greater than 1, i.e., all genes with a log2 fold change greater than 1 or less than -1, i.e., all genes with fold change below 0.5 or above 2. Then, in the results table, look at the log2FoldChange column to see which genes went up and which went down. Simon