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Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
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It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
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Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
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TPM is irrelevant for miRNA-seq; CPM works fine.
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"I'm also unsure what qualifies as a lateral gene."
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Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
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Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
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