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Comment: Bioconductor 3.20 Release Schedule
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randyprice13102000
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This offers much info
https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq
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ATpoint
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The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2
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ATpoint
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All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness
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ATpoint
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4.8k
> insert size, mean GC, etc...
This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness
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Gordon Smyth
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Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
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