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 sign? ). So, if someone already use WGCNA for this kind of data, I would have some questions: Firstly, are my data properly normalized? And secondly, how can I choose the maximal number of blocks for the blockWiseModule function ? I have access to a cluster, can I deduct the maxBlockSize when I know the available RAM?
Thanks in advance,
Have a nice day !
Enora
Thank you for your comment.
I said "nice" because, the curve saturates above the 0.9 line with a soft threshold of 14 or 16. The non-transformed beta values lead to a curve as good as with the transformed data so it's good. At the end, I used the 400K beta values with a maxBlockSize of 60K (128GB available) and it worked out fine. Peter Langfelder answered me here on Bioconductor support : https://support.bioconductor.org/p/121989/#122136
Enora