Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
EdgeR GLM linear regression of time series bsuac6 Bioinformatics 3 03-28-2013 02:50 PM
GATK: -glm DINDEL question Michael.James.Clark Bioinformatics 36 04-25-2012 11:39 AM
GLM in DESeq SMcTaggart Bioinformatics 3 12-10-2011 11:02 PM
question about glm in R tujchl Bioinformatics 3 11-28-2011 12:25 AM
BaySeq vs GLM in EdgeR and DESeq Hilary April Smith Bioinformatics 0 08-03-2011 10:14 AM

Thread Tools
Old 04-27-2012, 04:20 AM   #1
Junior Member
Location: -----

Join Date: Apr 2012
Posts: 1
Default edgeR - Run GLM on only one gene

I would like to use edgeR's GLM functionality to determine the influence of several factors on a gene's expression levels. For performance reasons I would like to estimate the dispersion using the entire count table, but then determine the fit just for the gene I am interested in.

Is there any way to do this, i.e. call glmFit() on just one row of the table? I already tried to create a new CDS for just the gene and copy over the dispersion from the full CDS, but that does not seem to work.
nnn is offline   Reply With Quote
Old 05-07-2012, 12:42 AM   #2
Gordon Smyth
Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91

If 'y' is your full DGEList object, with common or tagwise dispersions already estimated, you can simply use:

fit <- glmFit(y[i,], design)

where 'i' is any subset of genes you want, even a single gene. The dispersions are automatically subsetted for you.

Note that edgeR is a Bioconductor package, so you can get answers quickly by posting them to the Bioconductor mailing list.

Gordon Smyth is offline   Reply With Quote


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 06:31 PM.

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