Whenever I run WGCNA's pickSoftThreshold() on 22500 genes it is freezing the computer and is unable to complete the function. This problem exists whenever calculating connectivity for all the genes. Is there a way to process all the genes in smaller block sizes and still get a soft thresholding power?
1 answer
That is not usually the computationally heavy step. It shouldn't take so long as long as you are using a modern computer. Mine took minutes to finish the process and I had 20000 genes. The most computationally heavy step is the TOM calculation. That step could take many hours. I uploaded these jobs to servers for it to run... Or you can use the blockwiseModule() function to parallelize the process by roughly breaking genes to a few big modules first, which might give you slightly (or not) different results,
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