[BioC] pairwise.comparison invalid object for slot "pData"

[Crispin Miller]

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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