[Bioc-devel] R: Re: Deseq2 and differentia expression

Simon Anders anders at embl.de
Sat Jul 12 10:32:43 CEST 2014

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.


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