[BioC] using offsets from EDASeq and cqn for edgeR

[Gordon K Smyth]

Dear Mike,

edgeR uses the term 'offset' in the same way that has been standard for 
generalized linear models since Nelder and Wedderburn's original paper in 
1972.  It agrees with the meaning in the glm() function and in thousands 
of books and articles on glms.  It corresponds to your first formula for a 
glm with a log-link.

One should be very careful about using established technical terms in a 
way that conflicts with the established definition.

Best wishes
Gordon

------------------ original message
Wed Feb 20 10:11:45 CET 2013
Michael Love love at molgen.mpg.de
[BioC] using offsets from EDASeq and cqn for edgeR

But I think it would be desirable for packages on both sides of the
hand-off to provide an explicit formula for what is meant by "offset",
which could be one of:

log(mu) = X * beta + offset
log2(mu) = X * beta + offset
log(mu) + offset = X * beta
log2(mu) + offset = X * beta

best,
Mike

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