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Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
by
Gordon Smyth
52k
You should compute divided counts before estimating edgeR dispersions. These plots look like they are using raw counts.
You could also try…
Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde
by
Peter Hickey
▴
760
Thanks, Aaron.
The PR returns a better looking knee-point than the current default on my data (knee = 2363).
![knee-point from 124][1]
…
Answer: The default value of 'abundanceCol'
by
James W. MacDonald
68k
The default is dependent on the input. Mostly it's TPM, but for e.g., StringTie it's FPKM. You can always see the function body by typing t…
Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
by
mohammedtoufiq91
▴
10
@gordonsmyth thank you very much for the feedback. I will try to seek guidance from the author's of those packages as well. Anyways, this i…
Answer: Testing KO vs WT at day4/day14 with interactions in edgeR
by
Gordon Smyth
52k
If you are interested in KO vs WT for each timepoint, then you would much better off using the group-mean representation of the model inste…
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