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What is the difference between Normalized Expression in EdgeR vs DESeq2?

First, and most obviously, two independent methods will never fully agree. Second, while the DESeq2-related code in fact gets the normalized counts based on the size factors the edgeR/voom code ...
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Error in DESeq2 analysis with dimnames

What works is: dds = DESeqDataSetFromMatrix(countData = data.frame(tmpcounts), colData = tmpph, design = ~celltype) Mind the ...
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baseMean threshold

Adding my answer from the crosspost: I would not use the baseMean for any filtering as it is (at least to me) hard to deconvolute. You do not know why the baseMean is low, either because there is no ...
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