Hi I am unable to get the plotform table using fData on eset object downloaded from ArrayExpress. Here is the example R code. library(ArrayExpress) dataset.name="E-TABM-493" data=trygetAEdataset.name, type="processed")) cn=getcolproc(data) eset=procset(data, cn[2]) platform=fData(eset) The platform is not coming in table format. Thank You Sailu Yellaboina Visiting Fellow NIEHS, NIH [[alternative HTML version deleted]]

Dear Sailu you need to provide the output of "sessionInfo()" as well as the error message you get, or what eaxctly in the result that you get you think is wrong. What do you mean by "coming in table format"? Neither "coming" nor "table format" are well-defined concepts in the R language. When I just ran your code chunk, I got: > str(platform) 'data.frame': 45101 obs. of 17 variables: $ Composite.Element.Name : Factor w/ 45101 levels "Affymetrix:CompositeSequence:Mouse430_2:1415670_at",..: 45038 45039 45040 45041 45042 45043 45044 45045 45046 45047 ... $ Comment.AECompositeName. : Factor w/ 45101 levels "1415670_at","1415671_at",..: 45038 45039 45040 45041 45042 45043 45044 45045 45046 45047 ... $ ....[11 more elements] .... which seems alright to me. I also got, > eset=procset(data, cn[2]) Read 49 items Warning message: In eval(expr, envir, enclos) : Cannot attach phenoData > sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-10 r51966) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=la_AU.utf8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] ArrayExpress_1.9.0 Biobase_2.9.0 fortunes_1.3-7 loaded via a namespace (and not attached): [1] XML_3.1-0 affy_1.27.1 affyio_1.17.0 [4] limma_3.5.3 preprocessCore_1.11.0 Best wishes Wolfgang On 10/05/10 22:25, Sailu Yellaboina wrote: > Hi > I am unable to get the plotform table using fData on eset object > downloaded from ArrayExpress. > > Here is the example R code. > > library(ArrayExpress) > dataset.name="E-TABM-493" > data=try(getAEdataset.name, type="processed")) > cn=getcolproc(data) > eset=procset(data, cn[2]) > platform=fData(eset) > > The platform is not coming in table format. > > Thank You > Sailu Yellaboina > Visiting Fellow > NIEHS, NIH > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber