Hi [...] > res <-results(dds) > ddsNoPrior <- DESeq(ddHTSeq, betaPrior=FALSE) #only for lessABs > resGA <- results(ddsNoPrior, lfcThreshold=.5, altHypothesis="lessAbs") You again use the wrong thresholds. Are you sure you read my previous mail? > So What is wrong? I'm interest to have a list of genes are greater than 1 and > use as de.genes for the spia package. Here don't found difference!! Please explain exactly what you mean by "genes are greater than 1". What do you want to be greater than one? The fold change? the log2 of the fold change? or the absolute value of the log2 fold change? To be frank, your mail sounds a bit as if you are not quite clear on the different meaning of these three terms. (Sorry if this sounds patronizing but I have been asked similar questions so often that I no longer take for granted that people know what a logarithm is. I hope you do; otherwise, you won't get far.) S PS: Please do not cross-post to bioc-devel.