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Question: How to change sample names in featureCounts or edgeR
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gravatar for Gary
28 days ago by
Gary0
Gary0 wrote:

Hi,
I used STAR, featureCounts, and edgeR for RNA-Seq alignment, quantification, and differentially expressed analysis. Could you teach me how to change sample names, e.g. using Chuong533 instead of Users.gary.Documents.Project.20180429_ZebraFinchColor.20180508_Analysis.featurecounts.Chuong553.bam. Please see the detail below and many thanks.

Best,
Gary

The detail
http://68.181.92.180/~Gary/temporal/Bioconductor_20180617.txt

ADD COMMENTlink modified 28 days ago by Gordon Smyth34k • written 28 days ago by Gary0
1
gravatar for Gordon Smyth
28 days ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

Continuing the code I gave you previously ( How edgeR reads an R List object produced by featureCounts )

rc <- featureCounts(...)
y <- DGEList(rc$counts)
colnames(y) <- paste0("Chuong",553:656)

 

ADD COMMENTlink modified 28 days ago • written 28 days ago by Gordon Smyth34k

Thank you so much!

ADD REPLYlink written 28 days ago by Gary0
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