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Question: Results changed after DESeq2 upgrade
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gravatar for Shi, Tao
2.8 years ago by
Shi, Tao720
Shi, Tao720 wrote:

hi list,

I recently upgraded my R to 3.1.2 and DESeq2 to 1.6.3.  I re-run some of my code on a RNAseq experiment.  Comparing to the old results (done in R 3.1.0 and DESeq2 v1.4.5), all the estimates (e.g. fold changes, p values) have changed.  It seems that the most dramatic changes happened to those genes with large fold changes (I haven't checked carefully if these genes are those with low read counts).  Could somebody give me some pointers on what exactly changed between the two versions that would cause these changes?  I read through the package's news file and it wasn't obvious to me.

Thanks!

Tao

ADD COMMENTlink modified 2.8 years ago by Michael Love15k • written 2.8 years ago by Shi, Tao720
0
gravatar for Michael Love
2.8 years ago by
Michael Love15k
United States
Michael Love15k wrote:

hi Tao,

See the answer to this previous question:

Question about DESeq2 version updates

ADD COMMENTlink written 2.8 years ago by Michael Love15k

Thank you very much, Michael!

Tao

ADD REPLYlink written 2.8 years ago by Shi, Tao720
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