[BioC] ERRORS IN LIWONG EXPRESSION VALUES.

[Rafael A. Irizarry]

i dont know how dChip deals with it (its not open source), but the
algrotihm described in their paper doest always converge. its a
mathematical reality not necessarily an error with bioconductor code.

On Thu, 21 Aug 2003, Stephen Nyangoma wrote:

> Dear All, 
> I want to obtain expression values based on my data using Li-Wong
> method. I gave the following command 
> 
> liwongexpre<-expresso(Data2,normalize.method="invariantset",bg.correct=FALSE,
> pmcorrect.method="pmonly",summary.method="liwong")
> 
> It looks like I do not attain convergence. Is may call function ok?
> 
> 
> > Data2
> AffyBatch object
> size of arrays=640x640 features (12803 kb)
> cdf=MG_U74Av2 (12488 affyids)
> number of samples=4
> number of genes=12488
> annotation=mgu74av2
> >
> 
> 
> Data2<-ReadAffy(filenames=c("../M7SS02080619.CEL","../M7SS02080607.CEL")
> 
> > colnames(exprs(Data2))<- c("BXD5a","BXD9a")
> >
> liwongexpre<-expresso(Data2,normalize.method="invariantset",bg.correct=FALSE,pmcorrect.method="pmonly",summary.method="liwong")
> normalization: invariantset
> PM/MM correction : pmonly
> expression values: liwong
> normalizing...done.
> 12488 ids to be processed
> .........
> There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> > warnings()
> Warning messages:
> 1: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 2: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 3: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 4: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 5: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 6: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 7: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 8: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 9: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 10: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 11: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 12: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 13: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 14: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 15: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 16: No convergence achieved, too many outliers in: fit.li.wong(probes,
> ...)
> 
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