[BioC] simpleaffy pairwise.comparison problem

[David Ruau]

Hi Iain,

I am experiencing the same problem as you on a ExpressionSet generated  
from justRMA()
Did you found a solution?

Here is the session:
 > da.rma <- justRMA(celfile.path="CELfiles/" , destructive=TRUE,  
phenoData=pd)
 > da.rma
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 214 samples
   element names: exprs, se.exprs
phenoData
   rowNames:
[...]
 > class(pd)
[1] "data.frame"
 > pData(da.rma) <- pd
 > results <- pairwise.comparison(da.rma, "group", c("A","B"))
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"

 > sessionInfo()
R version 2.7.1 (2008-06-23)
i386-apple-darwin9.3.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices datasets   
utils     methods   base

other attached packages:
  [1] simpleaffy_2.16.0    gcrma_2.12.1         matchprobes_1.12.0    
genefilter_1.20.0    survival_2.34-1
  [6] hgu133plus2cdf_2.2.0 affy_1.18.2          preprocessCore_1.2.0  
affyio_1.8.0         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

On Feb 4, 2008, at 12:50 PM, IAIN GALLAGHER wrote:

> Hi List.
>
> I'm trying to use the simpleaffy pairwise.comparison procedure on  
> two groups of arrays. The groups are defined in the phenoData slot  
> under the heading 'group' and are indicated by numbers i.e.  
> 1,1,2,2,2,3,3,3 etc.
>
> If I try:
>
> results<-pairwise.comparison(test, 'group',c(1,4))
>
> where 'test' is an appropriate subset of the data I get the  
> following error:
>
> Error in validObject(.Object) :
>  invalid class "PairComp" object: 1: invalid object for slot  
> "members" in class "PairComp": got class "numeric", should be or  
> extend class "character"
> invalid class "PairComp" object: 2: invalid object for slot "pData"  
> in class "PairComp": got class "integer", should be or extend class  
> "data.frame"
>
> Is it possible to change the class of the 'group' indicators in my  
> phenoData slot or is there another way to get around this problem?
>
> Thanks
>
> Iain
>