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 > 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? Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}

Since you did not follow the posting guide and provide us with the output of sessionInfo (or just about any other detail that would help someone that is not looking directly over your shoulder) it is a bit hard to know if it is surprising or not - my guess is that it is not... 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 >> 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? > > Thanks -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

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_TELE PHONE=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 >