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Comment: Question on RNA-Seq single sample data analysis in EdgeR
by
Gordon Smyth
45k
You questions are answered by the edgeR documentation.
I must say that I thought you already understood that you have no replication and t…
Comment: DEseq2: working with unbalanced number of sample in tumor study?
by
sadiksha.adhikari
•
0
Hi, I have a similar problem in my analysis: 35 vs 800 samples. I found several posts where you have commented that "There is no problem wi…
Comment: Question on RNA-Seq single sample data analysis in EdgeR
by
mohammedtoufiq91
▴
10
@gordonsmyth Hi, thank you very much for the prompt response. Sure, I will create a `DGEList object` from a table of counts and samples >…
Answer: Question on RNA-Seq single sample data analysis in EdgeR
by
Gordon Smyth
45k
Yes, it is necessary to run `calcNormFactors`, as it always is for any DE analysis. It would also be sensible to filter non-expressed genes…
Comment: How to run GSVA with partially NA genes
by
blakebowen
•
0
I was a little worried about discarding so many genes, although sounds like this can't be helped. The results are still quite useful so I t…
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