[BioC] option rm.mask=TRUE in ReadAffy
laurent at cbs.dtu.dk
Tue Oct 28 14:52:17 MET 2003
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",
> 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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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
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".
More information about the Bioconductor