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Comment: Multi-factor paired RNAseq differential analysis with DEseq2
by
swbarnes2
▴
970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command
So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2
by
Matthew
•
0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this?
by
amir.khan
•
0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2
by
Michael Love
35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2
by
swbarnes2
▴
970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
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