Remove genes before normalization?
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@msladek
Last seen 2.9 years ago
United States

Hello, just a general question about filtering genes before normalization. I am comparing RNA-seq data for different single-gene deletion mutants with my wild type strain. Is it advisable to remove those genes which some strains are lacking from the count table? I read that you should remove genes that cannot possibly be expressed in all samples but I'm not sure if in this case it would bias the normalization.

Thanks,

-Maggie

edgeR • 644 views
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@gordon-smyth
Last seen 3 minutes ago
WEHI, Melbourne, Australia

No, there is no need to remove genes in this way.

I don't know where you may have read that you must remove genes that contain zero counts but the edgeR documentation does not advise that. The last thing you would want to do is to remove genes that are DE between your groups (e.g., expressed in one group but not the other) because those are exactly the genes that you would hope the DE analysis to detect.

It is advisable to remove genes that have low counts in all (or almost all) samples but that does not rule out zeros in individual samples. The filterByExpr function is provided to do the filtering.

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