WGCNA "expression data": raw counts, TPM or logTMP?
For my WGCNA analysis I need to use "expression data" for several functions. But it is not described whether this is raw count data or TPM values? Or even logTPM values? I have a scRNA Seq experiment, would it be ok to use the logTPM matrix as "expression data"?
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ly.leifels •
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I'm sorry if this is obvious, but here's the WGCNA tutorial; https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ The example expression data in there seems to be logTPM plus other stuff that you cut out.
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I wasn't sure. Thank you!
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Just to come to your queries since you have been putting a lot lately on WGCNA. Please read the tutorial carefully and then if you have any problem and face any issues, structure a question and we would be happy to help.
I edited your title for clarity. Also, when asking a question about WGCNA then a logic tag would be... 'WGCNA'. This helps developers find questions about their tools so you can get help.