[BioC] expresso errors for MBEI

[Rafael A. Irizarry]

ps - the next release (the devel version as well) will continue despite 
the error and give
you back an exprSet with values for the probesets were the algorithm
worked. 

attributes(eset3)$pps.warnings contains info on probesets that gave
problems

in version 1.1.1 you can run expresso and send all probenames, except the
problemtic ones, using the summary.subset argument.


On Wed, 14 May 2003, Rafael A. Irizarry wrote:

> 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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> > > 
> > 
> > 
> > 
> 
>