Hi, I found an error in the readBeadSummaryData function of beadarray. My code that worked in R 2.9.2 no longer works in R 2.11.1, and I also tried the code in the beadarrayUsersGuide(topic = "beadsummary") vignette. It also shows the same error (full code below): Error in grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) : unused argument(s) (extended = FALSE). I looked through the code of readBeadSummaryData, and twice the grep() function with extended=FALSE is used. If I just remove the extended=FALSE, then it appears to work, but then I get a warning (code also below). I'll use my hack fix for now, and see if any problems come up with the column names. Thanks, Jenny > dataFile = "SampleProbeProfile.txt" > sampleSheet = "SampleSheet.csv" > qcFile = "ControlGeneProfile.txt" > BSData = readBeadSummaryData(dataFile = dataFile, + qcFile = qcFile, sampleSheet = sampleSheet, + controlID = "TargetID") Error in grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) : unused argument(s) (extended = FALSE) #Read in a new function that's the same as readBeadSummaryData, but has the two instances # extended=FALSE removed from grep() functions > source("C:/Downloads/BeadSummaryExample(3)/JDBead.R") > BSData = JDBead(dataFile = dataFile, + qcFile = qcFile, sampleSheet = sampleSheet, + controlID = "TargetID") Warning messages: 1: In grep(colnames(QC[[i]]), colnames(exprs(BSData))) : argument 'pattern' has length > 1 and only the first element will be used 2: In grep(colnames(exprs(BSData)), samples) : argument 'pattern' has length > 1 and only the first element will be used > > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines tcltk grid stats graphics grDevices datasets utils methods base other attached packages: [1] lumi_1.14.0 MASS_7.3-6 mgcv_1.6-2 annotate_1.26.0 [5] WGCNA_0.92 Hmisc_3.8-2 survival_2.35-8 qvalue_1.22.0 [9] flashClust_1.00 dynamicTreeCut_1.21 impute_1.22.0 beadarray_1.16.0 [13] limma_3.4.4 affyQCReport_1.26.0 lattice_0.18-8 xtable_1.5-6 [17] simpleaffy_2.24.0 genefilter_1.30.0 made4_1.22.0 scatterplot3d_0.3-30 [21] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 gdata_2.8.0 [25] gtools_2.6.2 RColorBrewer_1.0-2 ade4_1.4-14 affyPLM_1.24.0 [29] preprocessCore_1.10.0 gcrma_2.20.0 affycoretools_1.20.0 KEGG.db_2.4.1 [33] GO.db_2.4.1 RSQLite_0.9-1 DBI_0.2-5 AnnotationDbi_1.10.1 [37] affy_1.26.1 Biobase_2.8.0 RWinEdt_1.8-2 loaded via a namespace (and not attached): [1] affyio_1.16.0 annaffy_1.20.0 biomaRt_2.4.0 Biostrings_2.16.6 Category_2.14.0 [6] cluster_1.12.3 GOstats_2.14.0 graph_1.26.0 GSEABase_1.10.0 hwriter_1.2 [11] IRanges_1.6.8 Matrix_0.999375-39 nlme_3.1-96 RBGL_1.24.0 RCurl_1.4-2 [16] tools_2.11.1 XML_3.1-0 > 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

Hi all, when I try to run affyQCReport on canine arrays, I get this error message: Error in setQCEnvironment(cdfn) : Could not find array definition file ' canine2cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. Any suggestions? Thanks for your time. Ina