Thread: DESeq2 error
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Old 09-07-2014, 01:08 AM   #4
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

That's actually a different error. So it seems that a parametric fit doesn't work well for this dataset. One possibility would be to use local fitting and increase the number of vertexes. I don't think there's a way to do that with DESeq2 (there was with DESeq), though you could modify the code a bit.

Your best bet would be to post this to the bioconductor email list and CC Michael Love, the DESeq2 maintainer. Please include the output of sessionInfo() in your email. It may turn that you'll need to send one of the DESeq2 authors your dataset so they can have a look.

As an aside, I probably wouldn't put too much effort into an experiment where you're just comparing two samples against each other (as appears to be the case from your sampleTable).
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