[BioC] LIMMA No residual using rmaPLM

Ben Bolstad bolstad at stat.Berkeley.EDU
Tue Sep 6 16:36:37 CEST 2005

Indeed, lmFit when it identifies a PLMset object tries to derive weights
using the se.chip.coef slot of the PLMset object. By default rmaPLM does
not return these but fitPLM would.

Looking back through your previous code it appears as though what you were
trying to do is compare situations where you gave absent probesets 0 weight
and everything else a weight of 1 with a situation where everything is
unweighted (ie essentially equal weights). You could carry out this second
situation by supplying a matrix of ones as your weights if supplying a
PLMset object or alternatively carryout RMA using rma() and supply the
resultant exprSet without weights to lmFit.


On Tue, 6 Sep 2005, Ron Ophir wrote:

> Thanks, Ben. I haven't seen your response probably due to problem in the
> way I send my e-mail or the way my e-mail address is subbmited to the
> server. Anyhow, what you mean that when lmFit identifies PLMset object
> it requires weights either from the PLMset object or by the users. And
> in the PLMset object that generated by rmaPLM does not supply weights.
> Is that so?
> Thanks,
> Ron
> II'd recommend that you use fitPLM rather than rmaPLM for these
> purposes.The reason why it is giving "reasonable results" in the first
> case andan error in the other case, is that it is using your user
> suppliedweights in the earlier situation and trying to derive some
> sensibleweights based on the PLM model fit. Unfortunately rmaPLM does
> not returnthe information that is used to construct these but fitPLM
> does.Ben

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