User: enora.fremy

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Posts by enora.fremy

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Comment: C: WGCNA soft threshold with methylation data but no scale-free topology
... Thank you for your prompt answer. The data seems OK. I think I'll take a beta of 20 (SFT.R.sq of 0.62 and mean connectivity of 2900). When you say "adjust for the cluster membership", do you mean the kME? And to adjust for the sex and age, do you think I can use something like ComBat() from the sv ...
written 3 months ago by enora.fremy0
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WGCNA soft threshold with methylation data but no scale-free topology
... Hi, I am doing WGCNA on methylation data (EPIC) from human blood samples and I'm stuck when choosing the soft threshold. I already made WGCNA on RNA-seq data before and the step of choosing the soft threshold was easy, with a high SFT.R.sq and a low mean connectivity (0.9 and 48). I selected the 2 ...
wgcna methylation scale-free topology epic written 3 months ago by enora.fremy0 • updated 3 months ago by Peter Langfelder2.3k
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Comment: C: WGCNA on methylation data
... Thanks a lot for your quick reply and your great job on WGCNA ! After several tests, I used a maxBlockSize of 60K with 128GB of RAM with the beta values. It worked out fine :) Enora ...
written 5 months ago by enora.fremy0
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WGCNA on methylation data
... Hello everyone, I am working on methylation data and I want to use WGCNA on them. The data are the beta values of 400K CpG probes and ~30 samples which were transformed by log2(beta+1) (The data then have a nice scale-free topology profile when the soft threshold is calculated, I think it is a good ...
normalization wgcna dna methylation written 5 months ago by enora.fremy0 • updated 5 months ago by Peter Langfelder2.3k

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