Thanks. That seemed to do it. That behavior is highly unexpected, at least to me. On Tue, May 1, 2012 at 10:35 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > You need to have consistent ordering between your phenoData and expression > matrix. > > Best, > > Jim > > > > > On 5/1/2012 1:18 PM, dha 2001 wrote: > >> Hi, >> >> I'm trying to create a small expression set from the following pieces of >> data: >> >> >> is.matrix(sdr) >>> >> [1] TRUE >> >> >> sdr >>> >> PR8.16 PR8.12 X31.12 PR8.24 VN.24 >> VN.12 >> 1600014C10Rik 0.1398317 -0.07606908 0.1183433 0.8794916 0.5701783 >> 0.2045793 >> 1700123I01Rik 0.2797059 0.17511382 0.2417623 0.9663656 0.7656528 >> 0.3691544 >> 2010005H15Rik 0.5722452 0.22999830 0.5018363 1.0000000 0.7351083 >> 0.5912760 >> X31.16 VN.16 X31.24 M.12 M.24 M.16 >> 1600014C10Rik 0.3294323 0.1177338 1.0000000 0 -0.1618993 -0.07646396 >> 1700123I01Rik 0.4761550 0.4523119 1.0000000 0 0.3090218 0.16773738 >> 2010005H15Rik 0.8050344 0.5789556 0.8703344 0 0.1371578 0.06224045 >> >> >> And >> >> >> repPhenoData >>> >> An object of class "AnnotatedDataFrame" >> rowNames: X31.12 PR8.24 ... VN.24 (12 total) >> varLabels: strain time >> varMetadata: labelDescription >> >>> pData(repPhenoData) >>> >> strain time >> X31.12 X31 12 >> PR8.24 PR8 24 >> PR8.12 PR8 12 >> PR8.16 PR8 16 >> VN.16 VN 16 >> M.12 M 12 >> M.24 M 24 >> X31.24 X31 24 >> VN.12 VN 12 >> M.16 M 16 >> X31.16 X31 16 >> VN.24 VN 24 >> >> As far as I can tell, the names match up: >> >> sort(sampleNames(repPhenoData)**) >>> >> [1] "M.12" "M.16" "M.24" "PR8.12" "PR8.16" "PR8.24" "VN.12" >> "VN.16" >> [9] "VN.24" "X31.12" "X31.16" "X31.24 >> >> sort(colnames(sdr)) >>> >> [1] "M.12" "M.16" "M.24" "PR8.12" "PR8.16" "PR8.24" "VN.12" >> "VN.16" >> [9] "VN.24" "X31.12" "X31.16" "X31.24" >> >> The objects appear to be valid: >> >> validObject(sdr) >>> >> [1] TRUE >> >>> validObject(repPhenoData) >>> >> [1] TRUE >> >> However, when I try to create the expression set, I get: >> >> eSDR<- new("ExpressionSet", exprs=sdr, phenoData=repPhenoData) >>> >> Error in validObject(.Object) : >> invalid class "ExpressionSet" object: sampleNames differ between >> assayData and phenoData >> >> >> Any clues? >> >> Thanks! >> >> -DHA >> >> sessionInfo() >>> >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ggplot2_0.9.0 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-17 RColorBrewer_1.0-5 colorspace_1.1-1 >> dichromat_1.2-4 >> [5] digest_0.5.2 grid_2.14.2 memoise_0.1 munsell_0.3 >> >> [9] plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1 scales_0.2.0 >> >> [13] stringr_0.6 tools_2.14.2 >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]