Results changed after DESeq2 upgrade
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago

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

deseq2 • 817 views
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@mikelove
Last seen 1 day ago
United States

hi Tao,

See the answer to this previous question:

Question about DESeq2 version updates

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Thank you very much, Michael!

Tao

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