WGCNA "expression data": raw counts, TPM or logTMP?

Question

[ly.leifels]

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"?

[ivivek_ngs]

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.

[WouterDeCoster]

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.

[ly.leifels]

I wasn't sure. Thank you!

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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Answer 1

[larvalanobium]

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.