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Answer: DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
It is unusual to see such a big difference between the two analysis methods, although it is more likely when you have only two replicates d…
Comment: Does DiffBind make consensus peaks sets for samples from a given condition (e.g.
You need to call `dba.normalize()` twice, first to establish the normalization calculations, and the second time to retrieve them: cou…
Answer: DiffBind on ATAC seq data
Within `DiffBind`, the main thing is to change the value of the `summits` parameter when calling `dba.count()`. The default value of 200 re…
Answer: Help with Error in DiffBind
This error is usually caused by incorrectly specifying the `PeakCaller` (or `ScoreCol` if present). What is the format of your peak file…
Answer: deseq2 normalization and statistical method
This is all answered in the vignette which you even reference (what DESeq() does, how to get normalized counts and to use raw counts). I al…
Answer: Can I run DESeq2 with SMART-Seq data
Comment: RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
A: Compare and filter two BAM files, one record at a time
Answer: Batch correction and Deseq2
Answer: How edgeR estimate the common dispersion?
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