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Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
by
Laurent Gatto
1.6k
Hmm, it is a bit surprising that you have so many the same scores. I would try to look at the actual spectra, and check the matching peaks,…
Comment: How to control batch effect if Group and batch are same?
by
ATpoint
★ 4.5k
Spam is strong in here.
Answer: How to control batch effect if Group and batch are same?
by
RasheedDickinson
• 0
Batch correction in cases where groups are confounded can be challenging. Considering advanced methods like RUV or sva might help in such s…
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
by
Gordon Smyth
51k
Thanks very much for the reproducible example. The bug has been fixed now in edgeR 4.3.17 on the Bioconductor developmental repository.
Answer: Highly DE genes but small count difference within conditions
by
h1vu81gcd7
• 0
It sounds like you're diving deep into DE analysis, comparing condition1 with the control using a solid design. However, the elevated padj …
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Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Trying to use enrichGO
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Answer: dmpFinder for other objects
GSVA ssGSEA vs. Broad implementation of ssGSEA
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