[BioC] expresso errors for MBEI

[Ann Hess]

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

> 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.

***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




> 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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> >
>
>
>