[BioC] using offsets from EDASeq and cqn for edgeR

[Kasper Daniel Hansen]

Mike has raised a couple of important issues wrt. using the output
from cqn as offsets in a GLM, for example by using edgeR.  We are
looking into this, and I'll make a follow up post when we have looked
at this in detail.

Kasper


On Wed, Feb 20, 2013 at 6:05 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> 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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