[BioC] DESeq Fold-Change calculation

[Simon Anders]

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