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Comment: replace cat with message in glmTreat when lfc = 0 by ATpoint ★ 4.9k

> but there is no way to capture this type of printing when you're fully aware of what is happening and don't want to see the messages (e.g…

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

Normalization or filtering are never done for subsets of samples in any limma or edgeR analysis. These things must always be done globally.

Answer: DESeq2 interactions by swbarnes2 ★ 1.4k

The simpler way to do the first four comparisons is to make a new column in colData that is temp_pollution, and specify that column alone a…

Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k

You are. The reason I pointed you to `forgeBSgenomeDataPkgFromTwobitFile` is because it's much simpler, doesn't require a seed file, and is…

Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by mat149 ▴ 80

I've tried the following, but I must be missing something: setwd("C:\\Users\\....\\wd\\dump\\seqs_srcdir") e122<-readDNA…

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