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Old 12-10-2013, 10:03 PM   #1
miaom
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Join Date: Oct 2012
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Default edgeR: how to calculate group average/means ?

I am trying edgeR now to find deferentially expressed genes.
I have run
d <- DGEList(counts=data,group=g,lib.size=libSizes)
d <- calcNormFactors(d)
d <- estimateCommonDisp(d)
d <- estimateTagwiseDisp(d)
d <- exactTest(d)
# d.final <- topTags(de.com,n = length(data[,1]))
and got some results like

logFC logCPM PValue
A1bg 1.168034660 -3.842894 0.4137326
A1cf 0.000000000 -Inf 1.0000000
A1i3 0.000000000 -Inf 1.0000000
A2m -0.003703085 4.419204 0.9421192
A3galt2 0.437990409 2.861665 0.2611483

But I'd like to know the average/mean of the gene expressions in each condition/groups?
It seems logFC it is different from "log2(rowMeans(GrpB)/ rowMeans(GrpA))" calculating from cpm() counts.

How should I do the calculation ?

Thanks!
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Old 12-31-2015, 07:08 AM   #2
xrao
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Have you found the answer? I am also curious. Thank you!
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Old 01-02-2016, 06:47 AM   #3
Schelarina
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Default

Do you need CPM per each sample after TMM normalization?
you could do something like this
cpm <- cpm(d, log=TRUE, lib.sizes=lib.sizes, normalized.lib.sizes = TRUE, prior.count=0.25)
if your cpm values are negative then you can set the prior.count to a different value
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Old 01-04-2016, 07:08 AM   #4
xrao
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Thank you! But we meant mean values for each group/condition.
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