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Hi all My name is Yehudit, I am from UCLA. I am new to this forum, and to microarray analysis - hope someone could help:) Goal: trying to analyze Illumina HT v4 arrays, but I have access only to the bead summary data, and was hoping to use "beadarray" package for analysis (should I use something else?). The tutorial on sample data worked just fine, so I moved to my data. I used GenomeStudio Gene expression to create 2 files: dataFile -data not normalized, no background subtraction. File includes TargetID, ProbeID + average signal, number of beads, beads std error and detection p value for each array. qcFile - control probes with the same info. These were read into BSData: > dataFile="5donors_nonorm_nobgd.txt" > qcFile="5donors_nonorm_nobgd_cotrolprobe.txt" > BSData = readBeadSummaryData (dataFile = dataFile, qcFile = qcFile,controlID = "ProbeID", sep="\t", skip = 0, qc.skip = 0, qc.columns = list(exprs = "AVG_Signal", Detection = "Detection Pval")) Warning message: In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, : controlIDs non-unique: 4 repeated entries have been removed. I ignored the warning message (as it seemed to remove the duplicates anyway), and tried to use channel to create another ExpressionSetIllumina object for plotting (as in tutorial). Here I got stuck: > channelNames(BSData)  "G" > BSData.ul<-channel(BSData,"G") Error in assayDataNew(exprs = exprs(object)[, selArray], se.exprs = se.exprs(object)[, : 'AssayData' elements with different rowNames In addition: Warning messages: 1: In eltRowNames == rownames(assayData[[elt]]) : longer object length is not a multiple of shorter object length 2: In eltRowNames == rownames(assayData[[elt]]) : longer object length is not a multiple of shorter object length Another question that I can't seem to find the answer to is how to create a second channel with log transformed data in the BSData? I am running Rstudio 0.96.122 with R 2.15. Thank you in advance, any help would be greatly appreciated! Yehudit Hasin, PhD David Geffen School of Medicine Dept. of Cardiology, Gonda 6524 UCLA phone: +1-310-2060133 email: yhasin at mednet.ucla.edu -- output of sessionInfo(): sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale:  C/en_US.UTF-8/C/C/C/C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  beadarray_2.6.0 ggplot2_0.9.1 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached):  AnnotationDbi_1.18.1 BeadDataPackR_1.8.0 DBI_0.2-5  IRanges_1.14.3 MASS_7.3-18 RColorBrewer_1.0-5  RSQLite_0.11.1 colorspace_1.1-1 dichromat_1.2-4  digest_0.5.2 grid_2.15.0 labeling_0.1  limma_3.12.0 memoise_0.1 munsell_0.3  plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1  scales_0.2.1 stats4_2.15.0 stringr_0.6  tools_2.15.0 -- Sent via the guest posting facility at bioconductor.org.