Hi Mark, Thanks a lot. I got it. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On May 3, 2012, at 6:33 AM, Mark Dunning wrote: > Hi, > > It looks like there is a typo in your command. The qc.columns argument > should be; > > qc.columns=list(exprs="AVG_Signal",Detection="Detection Pval") > > and you had mis-typed Dectection as Dectection. Sorry the error > message wasn't more informative in diagnosing the problem. The names > of the qc columns have to match the names in the ExpressionSet object > so that the control probes can get appended correctly to the main > expression matrix. > > Regards, > > Mark > > > On Tue, May 1, 2012 at 5:36 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >> Hi Mark, >> >> I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code: >> >>> library("beadarray") >> Loading required package: Biobase >> Loading required package: BiocGenerics >> >> Attaching package: ?BiocGenerics? >> >> The following object(s) are masked from ?package:stats?: >> >> xtabs >> >> The following object(s) are masked from ?package:base?: >> >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, >> pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', >> and for packages 'citation("pkgname")'. >> >> Loading required package: ggplot2 >> Welcome to beadarray version 2.6.0 >> beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details >>> setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput") >>> dataFile = "AsuragenMAQC-probe-raw.txt" >>> qcFile = "AsuragenMAQC-controls.txt" >>> BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID", skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detect ion Pval")) >> Error in QC[[index]] = data[[i]] : >> attempt to select less than one element >> In addition: Warning message: >> In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, : >> controlIDs non-unique: 6 repeated entries have been removed. >> >> and >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] beadarray_2.6.0 ggplot2_0.9.0 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 >> [7] grid_2.15.0 IRanges_1.14.2 limma_3.12.0 MASS_7.3-18 memoise_0.1 munsell_0.3 >> [13] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 RSQLite_0.11.1 scales_0.2.0 >> [19] stats4_2.15.0 stringr_0.6 >> >> Could you help me to figure out this problem? Thanks. >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu<mailto:jianhong.ou at="" umassmed.edu=""> >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor