[BioC] expresso errors for MBEI

[Rafael A. Irizarry]

it turns out the HU6800 array has two probesets
with just one probe pair:  

"HG2887-HT3031_at" 
"U90546_r_at"     

in this case the li and wong algorithm, as implemented in the affy
package, wont work. the li and wong model doesnt really apply. hopefully
the next release will incorporate a warning about this.

> On Wed, 7 May 2003, Ann Hess wrote:
> 
> > I am trying to use the expresso command to get MBEI values.  I get the
> > following errors.  Note that I was able to use expresso to get RMA and MAS
> > values for the same data without any errors.  Any suggestions?
> > 
> > **I am using R version 1.6.2 and affy version 1.1.1.
> > 
> > > eset3<-expresso(data,normalize.method="invariantset",bg.correct=FALSE,
> > 	pmcorrect.method="pmonly",summary.method="liwong")
> > 
> > normalization: invariantset
> > PM/MM correction : pmonly
> > expression values: liwong
> > normalizing...done.
> > 7129 ids to be processed
> > .Error in quantile.default(sigma.theta, normal.array.quantile) :
> >         Missing values and NaN's not allowed if `na.rm' is FALSE
> > In addition: Warning messages:
> > 1: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 2: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 3: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 4: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 5: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > Error in name.levels(cdf) : Object "cdf" not found
> > 
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> > 
> 
> 
>