EdgeR - default offset

drea11 · 08-15-2014, 11:11 AM

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!

dpryan · 08-15-2014, 03:02 PM

From the source code:

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).

Gordon Smyth · 08-18-2014, 12:48 AM

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.

drea11 · 08-18-2014, 06:20 AM

Thank you!

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08-15-2014, 11:11 AM	#1
drea11 Junior Member Location: Canada Join Date: Aug 2014 Posts: 9	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!

08-15-2014, 03:02 PM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	From the source code: 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).

08-18-2014, 12:48 AM	#3
Gordon Smyth Member 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.

08-18-2014, 06:20 AM	#4
drea11 Junior Member Location: Canada Join Date: Aug 2014 Posts: 9	Thank you!