[BioC] expresso errors for MBEI (fwd)

[Ann Hess]

Following up on errors when trying to Li Wong method:

> > 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))
[1] 0

>sum(!is.finite(exprs(data.n))
[1] 0