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Old 08-15-2014, 10:11 AM   #1
drea11
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Location: Canada

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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!
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Old 08-15-2014, 02:02 PM   #2
dpryan
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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).
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Old 08-17-2014, 11:48 PM   #3
Gordon Smyth
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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.
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Old 08-18-2014, 05:20 AM   #4
drea11
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Thank you!
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