Hi Everyone,

I am running a rna seq differential gene expression experiment with the following code:

dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Age+Gender+Response) dds <- DESeq(dds) res <- results(dds,contrast=c("Response","Yes","No"))

Looking at the results I get about thousands genes with absolute log fold change > 0.5.

However, when I run the following command:

resGA <- results(dds, lfcThreshold=0.5, altHypothesis="greaterAbs")

I only get 256 with absolute log fold change > 0.5.

Anyone can help me figure out what is the source of this discrepancy?

Thanks

Your first test is the following: pvalue is describing the probability that log fold change != 0, and the log fold change value is the most likely value given the data.

Your second test is: pvalue is describing the probability that the abs(log fold change value) < 0.5

You can therefore see how a gene with lfc of 0.51 may be significantly more than zero, but not significantly greater than 0.5