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Answer: When to use edgeR or limma
by
James W. MacDonald
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I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: Quality control of shotgun metagenomics data
by
James W. MacDonald
68k
This support site is meant primarily for helping people with technical questions about using Bioconductor packages. For general analysis qu…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR
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mohammedtoufiq91
▴
10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR
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Gordon Smyth
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Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
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