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

[Martin Morgan]

Hi David --

David Ruau <David.Ruau at rwth-aachen.de> writes:

> 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

There's no replication here, so no statistical conclusions can be
made. but...

>  > 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"

get.fold.change.and.t.test subsets a data frame without drop=FALSE, so
that when there is a single column (like in your x.rma) it produces a
vector rather than data.frame. So a work-around would be to add a
column to phenoData, e.g.,

lbl <- "Placeholder for simpleaffy workaround"
phenoData(x.rma)[["pseudo", labelDescription=lbl]] <- NA

Hope that helps,

Martin

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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