Simon, Yes, I was incorrect in saying that the FC calculation used unnormalized values. I have been given 2 equivalent datasets (8 controls and 8 treated) and need to "Show 'concordant' or reproducible hits". Using DESeq, dataset B gave only 21 (set B) transcripts significant compared to 431 for dataset A. Turns out That the stdev was higher for set B. Standard Deviation Dataset control treat A 76 130 B 96 164 The package edgeR is giving more usable results for the 2 datasets : 416 (A) and 145 (B) transcripts with 76 overlapping. Perhaps the variance Is controlled better in edgeR? Lana -----Original Message----- From: Simon Anders [mailto:anders@embl.de] Sent: Monday, August 27, 2012 2:11 AM To: Lana Schaffer; bioconductor at r-project.org Subject: Re: [BioC] DESeq Fold-Change calculation Hi Lana On 2012-08-26 13:16, Lana Schaffer wrote: > I haven't checked to see if there has already been a discussion about > the fold-change Calculation in DESeq, but I have found that the fold-change is calculated using the > Raw count values and not the normalized count values. I usually use the fold-change > With a cutoff value, but this isn't valid if the unnormalized counts are used for > The FC calculation. Any thoughts about this? Of course, fold change is calculated using the normalized counts -- unless you have uncovered a very strange bug. Could you demonstrate with an example what you mean? Cheers Simon