[BioC] option rm.mask=TRUE in ReadAffy

[Laurent Gautier]

On Tue, Oct 28, 2003 at 01:12:07PM +0100, weiss wrote:
> Hi everybody,
> 
> when I set  options    rm.mask=TRUE , rm.outlier=TRUE
> in the ReadAffy() routine
> 
> and then use
> 
> expresso(data, bgcorrect.method="rma",normalize.method="quantiles",
> pmcorrect.method="pmonly",summary.method="medianpolish")
> 
> I get thousands of messages
> "Error in if (converged) break : missing value where TRUE/FALSE needed"
> 
> and no expression values different from NA.
> 
> Does anybody know how to remove msked and outlier oligos from the analysis?
> 
> Thanks, Gunter
> 
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The "removal" of oligos set to NA is not directly possible
(I mean without some programming). The handling of NAs should
be done by the respective preprocessing methods you use. I
had a quick look and it seems that the normalization step goes
through the NAs ok (for the few I tried). The problem
is with the summary expression values methods. They should
handle missing values better I guess. For your particular
choices in expresso, try to see if you (or anyone) can fix 'medianpolish'.
(sorry, not much time these days).

Hopin' it helps

L.

PS: You should only get NAs for the probeset with one NA. If
you get NAs all across the exprSet returned by expresso, it
might mean that *very* large portions of at least one chip are "masked".