[BioC] Newer version of DESeq give much small list of DE genes

[Abhishek Pratap]

Hi Todd

I have seen this behaviour when I reduce the number of replicates to
0. I am assuming in your case with both the DESeq versions you are
using same number of replicates. Also in case you are not using
replicates at all then I believe it can affect the latest .DESeq
model. I am not sure about the version 1.2.

-Abhi

On Mon, Mar 12, 2012 at 3:11 PM, Creasy, Todd <tcreasy at som.umaryland.edu> wrote:
> Hi,
>
> We're comparing an older version of DESeq with the new 1.6 version and I'm finding a large discrepancy.  Probably an option I'm missing or something.  In the samples I'm working with, I see total DE genes going from ~200 - 2000 genes at FDR = 0.10 to nearly 0 genes using the new version at the same FDR.
>
> What could be going on here.  Admittedly, the old version was 1.2 so we were way behind but I'm still shocked by this drop off.
>
> Thoughts?
>
> todd
>
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