Hi,
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?

Lana Schaffer
Biostatistics, Informatics
DNA Array Core Facility
858-784-2263


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