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Comment: Interaction term vs grouping variable design considerations
by
Michael Love
41k
> is it correct that to extract this comparisions I would run... Yes, asking, 'is term X different than term Z' can be extracted with `res…
Answer: Interaction term vs grouping variable design considerations
by
Michael Love
41k
For questions about statistical analysis plan and interpretation, I recommend consulting with a local statistician or someone familiar with…
Answer: IgG control in RIP-seq with Deseq2
by
Michael Love
41k
You are mixing two threads of advice (I guess from different support site posts). You can just do the LRT then: ``` results(dds) ``…
Answer: Regressing out batch effects
by
Michael Love
41k
See Gordon's note above. Also in the DESeq2 vignette, in the FAQ, we show how to use limma's removeBatchEffect on VST values.
Answer: Not fully paired differential gene expression analysis
by
James W. MacDonald
65k
You removed samples because you had fewer than 5M reads? You might reconsider that decision. Unless the library sizes are really disparate,…
Votes
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: Obtaining pheno data from CEL files
Answer: permutation test in edgeR
Comment: permutation test in edgeR
DESeq2: Subset Results from 2-Factor Design
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