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Answer: single cell RNA seq pseudobulk batch correction by James W. MacDonald 67k

You can exclude the females from the non-responders.

Answer: Normalized counts to be used in decoupleR from deseq2 results by James W. MacDonald 67k

No, you never use normalized counts for anything but plotting. Can you point out the example that uses normalized counts?

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

If you care to know more about the process, there is a [GitHub with all the code][1]. It's pretty complicated though - the readme alone is …

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k

Thanks; I did not know which file exactly is being used. Good catch regarding the discrepancy between the 2 web pages. I will get in touch …

Answer: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

The data for the `OrgDb` packages comes directly from NCBI, and in this case the symbols come from the gene_info.gz file you [can get from …

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Comment: limma technical repeat correction

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Popular Question to Guido Hooiveld ★ 4.1k