[BioC] Trying to convert to ExpressionSet object problems

[Martin Morgan]

Daniel Brewer wrote:
 > Hello,
 >
 > I am having trouble converting an exprSet to an ExpressionSet.
 >
 >   
 >> U95B <- justGCRMA()
 >>     
 > ... Add various bits to the pheno data and change the name of the samples

(sorry about the first email, Daniel, please respond to this version 
which included the bioc mailing list).

What did you do? With an ExpressionSet (which is produced by current
software, below) you should

featureNames(U95B) <- ...

Feature names are stored in several places, and you've changed them in
some but not all, probably on the exprs but not se.exprs matrices in
assayData(U95B). Hence featureNames differ between AssayData members.
 >> class(U95B)
 >>     
 > [1] "exprSet"
 > attr(,"package")
 > [1] "Biobase"
 >   
 >> U95B <- as(U95B,"ExpressionSet")
 >>     
 > Error in validObject(.Object) : invalid class "ExpressionSet" object:
 > featureNames differ between AssayData members
 >
 >   
 > Anyone got any ideas what that means and how to fix it?  Also isn't it a
 > bit odd that justGCRMA produces the old type of object?
 >   
Probably you have an old version  of something

 > library(gcrma)
 > celpath = system.file("celfiles", package="affydata")
 > justGCRMA(filenames=list.files(celpath), celfile.path=celpath)
 > res = justGCRMA(filenames=list.files(celpath), celfile.path=celpath)
 > res
Computing affinities.Done.
Adjusting for optical effect...Done.
Adjusting for non-specific binding..Done.
Normalizing
Calculating Expression
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 2 samples
 element names: exprs, se.exprs
phenoData
 rowNames: binary.cel, text.cel
 varLabels and varMetadata:
   sample: arbitrary numbering
featureData
 featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at (22283 total)
 varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "hgu133a"


Here's my sessionInfo

 > sessionInfo()
R version 2.5.1 Patched (2007-08-01 r42387)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

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

other attached packages:
     gcrma matchprobes        affy      affyio     Biobase
   "2.8.1"     "1.8.1"    "1.14.2"     "1.4.1"    "1.14.1"

What's yours?

Martin

 > Thanks
 >