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Hi all,
I'm analyzing an RNA-seq data set for two different strains of Candida albicans across four time points and want to do WGCNA, but I only have TPM tables. The raw data exist (somewhere in our server...) but I'm unable to find them and just want to do WGCNA to have an idea of clusters I can look at. I've been working off of TPM tables generated by a previous grad student and have done all my DGE analysis using edgeR, but the output of a DGEList is psuedocounts which I can't really use outside of edgeR (as far as I understand it) and since I don't have the raw counts I can't use DESeq2. How would you all recommend going about this? I'm sure it can be done!!
WGCNA is not a Bioconductor package, but generally:
If you want to do serious analysis then find the raw data. There is no guarantee what the previous staff has done is proper. Process yourself to be sure data are reproducible.
TPM is not suited for edgeR, so output is not reliable.
I would really find the raw data, and then browse the WGCNA docs to see what they recommend in terms of input.