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User: pedrostrusso

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pedrostrusso30
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Posts by pedrostrusso

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Comment: C: WGCNA: relate modules to binary trait
... You're right, it doesn't look like you need the apply_vst parameter. About the qqplot, it looks like you could go either way... maybe Spearman could be a little more on the safe side, but I don't think Pearson would be a bad choice either. About the group comparisons, as you said before, both packa ...
written 5 weeks ago by pedrostrusso30
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Comment: C: WGCNA: relate modules to binary trait
... Hi Lin, sorry, I didn't notice the 5000 genes you used as input. Since you previously filtered your dataset, did you remember to include the *filter*=FALSE parameter in your *cemitool* function call? Otherwise, the function will filter your already filtered dataset, which would probably cause some b ...
written 5 weeks ago by pedrostrusso30
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Answer: A: WGCNA: relate modules to binary trait
... Hi Lin, thanks for using CEMiTool! CEMiTool's automatic filter is, as you may have noticed, quite stringent, and it tends to leave in the analysis mostly genes with significant activity in their given pathways. This is probably why you found that all your modules ended up being differentially expre ...
written 5 weeks ago by pedrostrusso30

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