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DESeq: question about baseMean. Also, replicates. Azazel Bioinformatics 5 05-18-2011 10:51 PM
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Another DESeq question shurjo Bioinformatics 2 05-15-2010 09:25 PM

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Old 05-18-2011, 07:26 PM   #1
Azazel
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Default DESeq: question about baseMean

In DESeq, what exactly is baseMean and how is it computed?

My guess is that baseMean is a kind of normalized tag count (however if that's correct they would probably call it something like tagMean or exprMean, not baseMean?!)

I read "Analysing RNA-Seq with the DESeq package", version from April 21, 2011 but can not find an explanation of baseMean.
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Old 05-18-2011, 10:48 PM   #2
Simon Anders
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Yes, it is the normalized count, i.e., simply the number of reads divided by the size factor (normalization constant) of the sample. I know that the name is not well chosen; this is why the term does not appear in the paper any more.
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Old 05-22-2011, 05:40 PM   #3
Azazel
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Hi Simon, thank you for your answers in this and the other thread. I would like to to suggest to leave the term in the documentation actually, but to explain it. Just from reading the DESeq vignette as it's now I think it's not clear what it is exactly.
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