[BioC] pairwise.comparison invalid object for slot "pData"
Crispin Miller
CMiller at picr.man.ac.uk
Wed Aug 6 13:14:46 CEST 2008
David,
I'll take a look at this and get back to you...
Crispin
On 5/8/08 13:47, "David Ruau" <David.Ruau at rwth-aachen.de> wrote:
> Dear List,
>
> I have a problem using the pairwise.comparison function in the
> simpleaffy package.
>> x.rma <- call.exprs(da, "rma")
> Background correcting
> Normalizing
> Calculating Expression
>> class(x.rma)
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>> pData(x.rma)
> population
> KO KO
> het het
>> results <- pairwise.comparison(x.rma, "population", spots=da)
> Error in validObject(.Object) :
> invalid class "PairComp" object: invalid object for slot "pData" in
> class "PairComp": got class "factor", should be or extend class
> "data.frame"
>
> I already posted this error a while a go but without obtaining any
> answer...
>
> If anybody has experienced the same problem and managed to solved it,
> I would appreciate that he or she share his solution...
>
> Best,
> David
> ---
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-apple-darwin9.4.0
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/C
>
> attached base packages:
> [1] splines tools stats graphics grDevices datasets
> utils methods base
>
> other attached packages:
> [1] mouse4302cdf_2.2.0 simpleaffy_2.16.0 gcrma_2.12.1
> matchprobes_1.12.0 genefilter_1.20.0
> [6] survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1
> affyio_1.8.1 Biobase_2.0.1
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.2.2 DBI_0.2-4 RSQLite_0.6-9
> annotate_1.18.0 tcltk_2.7.1
>
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