Entering edit mode
David Ruau
▴
190
@david-ruau-1562
Last seen 10.3 years ago
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