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Question: How edgeR reads an R List object produced by featureCounts
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gravatar for Gary
3 months ago by
Gary0
Gary0 wrote:

Hi,
I analyze 20 zebra finch RNA-Seq data, using STAR for alignment, Rsubread-featureCounts for quantification, and edgeR for differentially expressed analysis. However, I don’t know how to run edgeR to read an R List object produced by featureCounts (the detail below). Our study is a three-factor factorial experimental design. I also show the group information below. Could you help me? Many thanks.
Best,
Gary

Group information

Sample Sex Region Color
Chuong553 Male Cheek Red
Chuong554 Male Head Gray
Chuong555 Female Cheek Gray
Chuong556 Female Head Gray
Chuong557 Male Cheek Red
Chuong558 Male Head Gray
Chuong559 Female Cheek Gray
Chuong560 Female Head Gray
Chuong561 Male Cheek Red
Chuong562 Male Head Gray
Chuong563 Female Cheek Gray
Chuong564 Female Head Gray
Chuong649 Male Cheek Red
Chuong650 Male Cheek Red
Chuong651 Male Cheek Black
Chuong652 Male Cheek Black
Chuong653 Male Cheek White
Chuong654 Male Cheek White
Chuong655 Male Head White
Chuong656 Male Head White

 

R commands & error messages
http://68.181.92.180/~Gary/temporal/Rcommend.txt

 

ADD COMMENTlink modified 3 months ago by Gordon Smyth35k • written 3 months ago by Gary0
2
gravatar for Gordon Smyth
3 months ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

Feature counts just produces an R object (a simple list) so there is need to read anything. It doesn't write anything to disk. You just use the object directly in your R session, for example

fc <- featureCounts(...)
y <- DGEList(fc$counts)

See for example the section called "Quantifying Read Counts for each Gene" in the edgeR workflow or else the small case study here: http://bioinf.wehi.edu.au/RNAseqCaseStudy

ADD COMMENTlink modified 3 months ago • written 3 months ago by Gordon Smyth35k

Thank you so much.

ADD REPLYlink written 3 months ago by Gary0
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