Bioconductor Peakdata

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Normalization Peakdata DiffBind Cut&Tag

updated 2.9 years ago by ATpoint ★ 4.9k • written 2.9 years ago by bhandary.8590 ▴ 20

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Answer: DESeq2 used with zinbwave weights - Differences on contrasts calculations by eja.gsee.r.m • 0

Hi your issue with DESeq2 contrasts and zinbwave weights sounds like it might stem from how weights are integrated during the different con…

Comment: How to analyze Affy data, CEL files not available by eja.gsee.r.m • 0

When analyzing data without raw files like Bobby MAS expression measures t important to work within the limits of the available informatio…

Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k

What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…

Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…

Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740

@atpoint Should I first standardise data and then average replicates?

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