Help with WGCNA pickSoftThreshold error
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6.4 years ago

Hello, I'm running a GCRMA normalized data set through WGCNA. I've carefully followed the tutorial, including removal of NAs and outlier samples. When I ran the pickSoftThreshold function I received the following error:

> sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)
pickSoftThreshold: will use block size 17772.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 17772 of 17772
Error in datk[c(startG:endG), ] = foreach(t = actualThreads, .combine = rbind) %dopar%  :
  number of items to replace is not a multiple of replacement length

I'm fairly new to R, so am not sure how to diagnose this problem. I have used WGCNA on other datasets in the past without any problems, so this is new to me. What to do, gurus? Thanks!!!

R WGCNA • 8.0k views
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Apologies. I opened this in R rather than R studio after enabling multi-threading, and it ran without incident.

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I have no idea why that would work, but it worked for me, too. Good thinking :)

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3.5 years ago
quanta123 ▴ 100

Please use allowWGCNAThreads() replace enableWGCNAThreads() in RStudio.

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Saved me here. That would have taken me a long time to figure out.

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