Dear Mark and other beadarray users, I have some problems when trying to read in 24 samples of BeadChip data using the readBeadSummaryData function (beadarray v1.2.2, see below for complete sessionInfo). Everything works fine if I have only file containing the raw bead summary values for 24 arrays. However, when the bead summary values are in separate files for each array, calling readBeadSummaryData fails with: Error in names(a$exprs) : object "a" not found > traceback() 3: names(a$exprs) 2: gsub("AVG_Signal.(.+)", "\\1", names(a$exprs)) 1: readBeadSummaryData(targets, skip = 0) Looking into the code of readBeadSummary, variable "a" is indeed never initialized if readAcross = FALSE (as is the case here). Similarly, if the bead summary values are in three separate files for each group of eight arrays (columnwise from a Human_RefSeq-8 chip) readBeadSummaryData fails. This time variable "a" in readBeadSummary is defined since readAcross = TRUE but variable "a" is assigned to only once, namely for the first batch of eight arrays. The final BeadSummaryList object that is returned by readBeadSummaryData, therefore contains only information from the first eight arrays and ignores the remaining 16 arrays. Does anybody have any suggestions how to correct this? Best, Perry PS: Mark, I can make scripts and data available off the BioC discussion list if you want to reproduce the problem > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-solaris2.10 locale: C attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: beadarray affy affyio Biobase limma "1.2.2" "1.12.1" "1.2.0" "1.12.2" "2.9.1" --- Perry Moerland, PhD Room J1B-206, Bioinformatics Laboratory Department of Clinical Epidemiology, Biostatistics and Bioinformatics Academic Medical Centre, University of Amsterdam Postbus 22660, 1100 DD Amsterdam, The Netherlands