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Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
by
Michael Love
42k
If you have other covariates, you can't compare the counts directly. The batch and score influence the expected counts.
Comment: DESeq2 and shrinkage of log2 fold changes
by
Michael Love
42k
It is not enabled by default since 2016. The above post was written before that.
Answer: modelGeneVarByPoisson error selecting bandwidth automatically
by
Peter Hickey
▴ 740
Without a reproducible example or access to the data, it's a bit hard to say. I assume the examples work for you (`example("modelGeneVarBy…
Comment: DESeq2 and shrinkage of log2 fold changes
by
Shannon
• 0
Hi Mike, would you mind clarifying where the lfcShrink is enabled "by default"? As you also mentioned above "The difference between results…
Comment: SeSAMe DMR for EPIC V2
by
zhouwanding
▴ 10
My guess is that the input has a suffix-removed probe id for EPICv2 data. We will add a fix to that in the DMR function in a few days. But …
Votes
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: DESeq2 - vst() - log2FC - no replicates
Answer: Warning message when running limma with covariates
Answer: Warning message when running limma with covariates
Comment: Limma with covariates
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