DEXseq for larger samples
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Peter • 0
@peter-6856
Last seen 4.6 years ago
China

I am using DEXseq for larger samples 70 vs 80. I always got a error. I found a solution at: Efficiently running DEXSeq for Large Cohorts But I think it is out of date.
My code and error are follow.

dxr <- DEXSeq(dxd2, BPPARAM=MulticoreParam(workers=50))

Error in value[[3L]](cond) : setting worker timeout:
  error reading from connection
In addition: Warning message:
In rm(list = cuid, envir = env) : object '1' not found

dexseq • 1.4k views
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I'd be surprised if having many workers is helpful. Have you investigated how performance changes with SerialParam() an then MulticoreParam() with just a few (2, 5, 10) workers?

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@gordon-smyth
Last seen 43 minutes ago
WEHI, Melbourne, Australia

You haven't had any answers in a couple of days, so I'll suggest an alternative approach. You could consider using the voom() and diffSplice() functions in the limma package. These have comparable capabilities to DEXSeq but will run in seconds, even with large numbers of samples, and without any need for multiple cores.

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