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Comment: DESeq2 ML Query
by
chris2.a.white
• 0
Thank you Mike. Re: "The VST or scaled counts should be fine." So either the DESeqTransform object following VST, or the txi object (txi…
Comment: Advice on appropriateness of an offset in glmGamPoi/edgeR
by
Constantin Ahlmann-Eltze
▴ 30
Oh, I never realized. That's cool. Thanks for correcting me :)
Comment: Deseq2 use fpkm
by
Michael Love
42k
> this would not be between sample normalised You can directly compare TPM across samples for visualization etc. Gene level TPM can be ob…
Comment: Advice on appropriateness of an offset in glmGamPoi/edgeR
by
Michael Love
42k
Do you mean an offset matrix in the GLM? DESeq2 has `normalizationFactors` for this, and it can be combined with sequencing depth control u…
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR
by
Constantin Ahlmann-Eltze
▴ 30
Hi Alec, The problem you describe sounds related to problems that people encounter working with spatial data, where suboptimal segmentatio…
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Comment: Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connec
running apeglm on a normal model and multiple coefficients
Answer: SeSAMe DMR for EPIC V2
A: DESeq2: Is it necessary to include all terms and interactions in LRT tests?
A: Unable to download "BSgenome.Hsapiens.UCSC.hg19" package using R 3.6.3 on Window
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