Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
ASCII offset Bakhtiyar Taghizada Illumina/Solexa 4 03-11-2014 07:53 AM
Trimmomatic - default settings? Zapages Bioinformatics 1 01-04-2014 06:39 AM
"Offset" in the correlation between two ChIP-seq biological replicates inesdesantiago Bioinformatics 8 02-27-2013 08:20 AM
edgeR separate offset values/normalizations for each tag sruddy RNA Sequencing 1 07-08-2011 03:59 PM
bwa aln fred score offset offsetoff Bioinformatics 1 06-14-2011 02:14 PM

Thread Tools
Old 08-15-2014, 10:11 AM   #1
Junior Member
Location: Canada

Join Date: Aug 2014
Posts: 9
Default EdgeR - default offset

Greetings R aficionados!

I was wondering whether anyone could tell me what the default offset is that is used in the glmFit function of EdgeR? Is it either the library size, or lib.size*norm.factor(from calcNormFactors)?

Thanks for the help!
drea11 is offline   Reply With Quote
Old 08-15-2014, 02:02 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

From the source code:

#       Check offset and lib.size
        if(is.null(offset)) {
                if(is.null(lib.size)) lib.size <- colSums(y)
                offset <- log(lib.size)
So, log(lib.size).
dpryan is offline   Reply With Quote
Old 08-17-2014, 11:48 PM   #3
Gordon Smyth
Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91

If y is a matrix, then offset defaults to log(lib.size).

If y is a DGEList, then offset defaults to y$offset if that is set, otherwise to log(lib.size*norm.factors). See getOffset.

In other words, it defaults to whatever can be found in y.
Gordon Smyth is offline   Reply With Quote
Old 08-18-2014, 05:20 AM   #4
Junior Member
Location: Canada

Join Date: Aug 2014
Posts: 9

Thank you!
drea11 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 08:53 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO