[BioC] expresso errors for MBEI

[Laurent Gautier]

On Wed, May 07, 2003 at 12:54:42PM -0600, Ann Hess wrote:
> Here is what I got:
> 
> > immediately before the call to expresso that gives errors try
> 
> 
> > print(data)
> AffyBatch object
> size of arrays=536x536 features (8982 kb)
> cdf=Hu6800 (7129 affyids)
> number of samples=4
> number of genes=7129
> annotation=hu6800
> notes=
> > class(data)
> [1] "AffyBatch"
> > test1 <- normalize(data,method="invariantset")
> > test1
> AffyBatch object
> size of arrays=536x536 features (8982 kb)
> cdf=Hu6800 (7129 affyids)
> number of samples=4
> number of genes=7129
> annotation=hu6800
> notes=
> > test2 <- expresso(data,normalize.method="quantiles",bg.correct=FALSE,
> +        pmcorrect.method="pmonly",summary.method="liwong")
> normalization: quantiles
> 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: There were 11 warnings (use warnings() to see them)
> Error in name.levels(cdf) : Object "cdf" not found

THis is odd. Could you do:

data.n <- normalize(data, method="quantiles")

sum(is.na(exprs(data.n))

sum(!is.finite(exprs(data.n))


> 
> > warnings()
> 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, ...)
> 
> 
> > ps the non convergence warning is something you have to live with when
> > using li and wongs method. sometimes their algorithm doesnt converge. its
> > usually a very small percentage of the probesets though.


note: the devel version of the pack returns the genes for which a problem
occurred (associated attribute).

> 
> ***OK, but the call doesn't seem to return anything:
> > exprs(eset)[1:100,]
> Error in exprs(eset) : Object "eset" not found
> ***OR
> > test2
> Error: Object "test2" not found
> 

This is normal. An error interrupted the 'making' of the eset in the middle.


L.

 
> 
> 
> 
> > 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
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> >
> >
> >
> 
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