[BioC] error creating new exprSet

[Martin Morgan]

The change is in the Biobase package, which affy et al rely
on. Biobase now checks to make sure the objects it creates are valid,
in this case that the number of exprs columns (i.e., samples) equals
the number of pData rows.

When you say

> good.eset = new("exprSet", exprs = good)

exprSet sees that it's supposed to create an instance with 20 samples,
but how can it create the corresponding phenoData? From this:

> dim(pData(data))

it looks like you have a phenoData object that you want to associate
with your exprs data. So...

good.eset = new("exprSet", exprs=good, phenoData=data)

(perhaps data is an exprSet, and you need to provide phenoData(data)
as the value of phenoData) should do the trick.

Notice that in the old version

>good.eset = new("exprSet", exprs = good)
>good.eset
Expression Set (exprSet) with 
         7420 genes
         20 samples
                  phenoData object with 0 variables and 0 cases
          varLabels

you've generated an invalid exprSet -- no description of the
phenotypes associated with your samples!

Hope that helps

Martin

kfbargad at ehu.es writes:

> Dear list,
>
> I tried to create a new exprSet from my filtered Affy genelist using R 
> 2.3.0 with
> affy "1.10.0"
> simpleaffy "2.6.0"
> genefilter "1.10.0"
>
> and I got the folowing error:
>
> good.eset = new("exprSet", exprs = good)
> Error in validObject(.Object) : invalid class "exprSet" object: number 
> of exprs columns different from number of pData rows
>
> But
> dim(good)
> [1] 7420   20
> dim(pData(data))
> [1] 20  1
>
> I moved then to R version 2.2.0, 2005-10-06
> affy "1.8.1"
> simpleaffy "2.4.2"
> genefilter "1.8.0"
>
> and the very same commands gave me no error.
>>good.eset = new("exprSet", exprs = good)
>>good.eset
> Expression Set (exprSet) with 
>         7420 genes
>         20 samples
>                  phenoData object with 0 variables and 0 cases
>          varLabels
>
>
> Have I missed some critical changes in the new versions of the 
> packages?
>
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