Trouble pickSoftThreshold() large dataset WGCNA
0
1
Entering edit mode
@sventhedestroyer-9715
Last seen 8.1 years ago

I am currently trying to analyze a large dataset with WGCNA. I have ~400 samples that were run on the Illumina 450k array. Thus I have a matrix that is used in the soft thresholding that is ~400x450k. I'm using my University's cluster that has plenty of power. I've done some testing by subsetting my maxtix out to be 400x10000 with no problem. It took about 10min total. However, when I subset out to 400x100000 WGCNA gets stuck on the first block of probes (I let it go for an hour). For both I set my blockSize = 4000. Example code below.

sft = pickSoftThreshold(testdatExpr, powerVector = powers, verbose = 5, blockSize = 4000)

My question is if anyone has had experience analyzing this array (or a large one like it) that might have suggestions on what might be going on. Are there any diagnostics that I can run on my matrix to help figure it out (other than str())?

I am a relatively new user to WGCNA, but have done multiple complete analyses before this, and an intermediate R user.

r wgcna • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 566 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6