Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
DEXSeq - condition / group level average miaom RNA Sequencing 1 12-09-2013 08:48 PM
edgeR: very low p-value and very high variance within the group of replicates. What's valei Bioinformatics 1 06-23-2013 11:49 PM
How to find elements in group comparison A but not B in EdgeR? carmeyeii Bioinformatics 1 08-26-2012 11:47 PM
how to calculate average gap size odoyle81 Bioinformatics 10 01-20-2012 09:01 AM
what does it means Moodi Genomic Resequencing 2 01-24-2011 04:55 PM

Thread Tools
Old 12-10-2013, 10:03 PM   #1
Location: ca

Join Date: Oct 2012
Posts: 11
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)
# <- topTags(,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 ?

miaom is offline   Reply With Quote
Old 12-31-2015, 07:08 AM   #2
Junior Member
Location: Houston USA

Join Date: Mar 2014
Posts: 9

Have you found the answer? I am also curious. Thank you!
xrao is offline   Reply With Quote
Old 01-02-2016, 06:47 AM   #3
Location: P

Join Date: Apr 2014
Posts: 18

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
Schelarina is offline   Reply With Quote
Old 01-04-2016, 07:08 AM   #4
Junior Member
Location: Houston USA

Join Date: Mar 2014
Posts: 9

Thank you! But we meant mean values for each group/condition.
xrao is offline   Reply With Quote

edger, rnaseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:50 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO