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Comment: Which input file is used for DGEList in EgdeR?
by
mohammedtoufiq91
▴
10
Thank you @gordonsmyth
My collaborator asked me to test this pipeline with `egdeR` package. We are interested at gene level analysis only…
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Gordon Smyth
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I think it is a good idea to start a discussion with correct information. Looking back through Bioconductor Support records, it is not at a…
Comment: How to identify top most variable genes from log2 normalized data?
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Gordon Smyth
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Your code doesn't look right to me. I think you're using order() where sort() would be more appropriate.
To order your cpm matrix by row v…
Comment: How to load fasta file with openPrimeR?
by
Santiago Edilberto
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0
> library(openPrimeR)
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please mak…
Answer: Which input file is used for DGEList in EgdeR?
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Gordon Smyth
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I use and recommend featureCounts. Despite all that has been written on this topic, I still think that direct gene counting is faster and m…
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