Hi Mark and others, I was trying to get familiar with the beadarray package, and I was going through the beadsummary topic vignette: beadarrayUsersGuide(topic = "beadsummary") . I downloaded the example data as indicated in the vignette, and unzipped them into my working directory. However, I get a warning when reading in the data that it could not reconcile the dataFile with the sampleSheet information (full code and sessionInfo() below). This isn't a problem for much of the vignette, but the code for section 4 Differential Expression no longer works. I looked at the SampleSheet.csv file and compared the Sentrix_ID names to those in the columns in SampleProbeProfile.txt and they look the same, so I'm not sure why the code is no longer working. Thanks, Jenny > library(beadarray) Loading required package: limma Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: geneplotter Loading required package: lattice Loading required package: annotate Loading required package: AnnotationDbi Loading required package: xtable KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: hwriter Loading required package: sma Attaching package: 'beadarray' The following object(s) are masked from package:limma : backgroundCorrect, imageplot, plotMA > beadarrayUsersGuide(topic = "beadsummary") [1] "C:/PROGRA~1/R/R-28~1.0/library/beadarray/doc/beadsummary.pdf" > dataFile = "SampleProbeProfile.txt" > sampleSheet = "SampleSheet.csv" > qcFile = "ControlGeneProfile.txt" > BSData = readBeadSummaryData(dataFile = dataFile, + qcFile = qcFile, sampleSheet = sampleSheet, + controlID = "TargetID") Warning message: In readBeadSummaryData(dataFile = dataFile, qcFile = qcFile, sampleSheet = sampleSheet, : Could not reconcile dataFile with sampleSheet information. sampleSheet ignored. From section 4: > samples = pData(BSData.quantile)$Sample_Group > samples NULL > ?readBeadSummaryData > samples = as.factor(samples) Error in as.vector(x, mode) : invalid 'mode' argument > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 [4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [7] AnnotationDbi_1.4.1 lattice_0.17-15 Biobase_2.2.1 [10] limma_2.16.3 loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.0 KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RSQLite_0.7-1 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu

Dear Jenny, Thanks for the note - it appears that the zip file on our website contains a different dataFile to the one used to generate the vignette. I have updated this now, so try downloading the file again. With the correct file, you should be able to proceed without this warning. Best wishes, Matt >Hi Mark and others, > >I was trying to get familiar with the beadarray package, and I was >going through the beadsummary topic vignette: >beadarrayUsersGuide(topic = "beadsummary") . I downloaded the >example data as indicated in the vignette, and unzipped them into my >working directory. However, I get a warning when reading in the data >that it could not reconcile the dataFile with the sampleSheet >information (full code and sessionInfo() below). This isn't a problem >for much of the vignette, but the code for section 4 Differential >Expression no longer works. I looked at the SampleSheet.csv file and >compared the Sentrix_ID names to those in the columns in >SampleProbeProfile.txt and they look the same, so I'm not sure why >the code is no longer working. > >Thanks, >Jenny > > > library(beadarray) >Loading required package: limma >Loading required package: Biobase >Loading required package: tools > >Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >Loading required package: geneplotter >Loading required package: lattice >Loading required package: annotate >Loading required package: AnnotationDbi >Loading required package: xtable >KernSmooth 2.22 installed >Copyright M. P. Wand 1997 >Loading required package: hwriter >Loading required package: sma > >Attaching package: 'beadarray' > > > The following object(s) are masked from package:limma : > > backgroundCorrect, > imageplot, > plotMA > > > > beadarrayUsersGuide(topic = "beadsummary") >[1] "C:/PROGRA~1/R/R-28~1.0/library/beadarray/doc/beadsummary.pdf" > > > dataFile = "SampleProbeProfile.txt" > > sampleSheet = "SampleSheet.csv" > > qcFile = "ControlGeneProfile.txt" > > BSData = readBeadSummaryData(dataFile = dataFile, >+ qcFile = qcFile, sampleSheet = sampleSheet, >+ controlID = "TargetID") >Warning message: >In readBeadSummaryData(dataFile = dataFile, qcFile = qcFile, >sampleSheet = sampleSheet, : > Could not reconcile dataFile with sampleSheet information. >sampleSheet ignored. > > From section 4: > > samples = pData(BSData.quantile)$Sample_Group > > samples >NULL > > ?readBeadSummaryData > > samples = as.factor(samples) >Error in as.vector(x, mode) : invalid 'mode' argument > > > > sessionInfo() >R version 2.8.0 (2008-10-20) >i386-pc-mingw32 > >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >attached base packages: >[1] tools stats graphics grDevices utils datasets methods >[8] base > >other attached packages: > [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 > [4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 > [7] AnnotationDbi_1.4.1 lattice_0.17-15 Biobase_2.2.1 >[10] limma_2.16.3 > > loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.0 > KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RSQLite_0.7-1 > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: drnevich at illinois.edu