WGCNA input file

Question

[mxlsherry1992]

Dear all, after RNA-SEQ analysis, (RSEM, align_and_estimate_abundance.pl, abundance_estimates_to_matrix.pl and so on..) I got several files:

genes.TMM.EXPR.matrix

genes.TPM.not_cross_norm

I want to do WGCNA analysis next, so which file should I use for WGCNA analysis or none of the file can be used?

Thank you!

Answer 1

[Sej Modha]

Please see related thread: Where to find WGCNA tutorials? and Kevin's answer about a WGCNA tutorial that may help: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/