[BioC] DESeq Fold-Change calculation

Simon Anders anders at embl.de
Mon Aug 27 11:10:43 CEST 2012

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?


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