I am using beadarray to read in raw data from two Illumina mouse 6 bead chips. I am trying to read in 4 arrays (two arrays per sample) per chip. However, there is a problem I didn't manage to solve when I try to combine the data sets from two different chips. Combining the different data sets works if I don't give anything for the 'arrayNames' parameter in readIllumina() but then all the files in the directory are read. This small data set is only for testing and in the future I would like to combine many chips into one object, not necessarily including every sample on each array. Thanks in advance, Asta Below is the code and session information. --- library(beadarray) data <- readIllumina(path="1735640017", textType=".txt", arrayNames=c("1735640017_A_1", "1735640017_A_2", "1735640017_D_1", "1735640017_D_2") ) Found 4 arrays Reading pixels of 1735640017/1735640017_A_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640017/1735640017_A_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640017/1735640017_D_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640017/1735640017_D_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract data <- createBeadSummaryData(data, imagesPerArray = 2) exprs(data)[1:10,] 1735640017_A_1 1735640017_D_1 10243 148.28308 157.3592 10280 96.39223 108.3309 10575 132.72321 136.9459 20048 106.45987 125.9253 20296 12385.10467 11879.6216 20343 470.61351 293.3878 20373 114.44354 133.7846 20431 25695.85350 30478.6505 50008 607.38792 631.1659 50014 86.33236 89.1350 data2 <- readIllumina(path="1735640018", textType=".txt", arrayNames=c("1735640018_A_1", "1735640018_A_2", "1735640018_D_1", "1735640018_D_2") ) Found 4 arrays arrayNames(dataReading pixels of 1735640018/1735640018_A_1_Grn.tif 2) Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640018/1735640018_A_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640018/1735640018_D_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract Reading pixels of 1735640018/1735640018_D_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = subtract data2 <- createBeadSummaryData(data2, imagesPerArray = 2) exprs(data2)[1:10,] 1735640018_A_1 1735640018_D_1 10243 147.6654 153.04544 10280 113.3786 101.17059 10575 130.5891 123.23560 20048 113.0089 114.82174 20296 12992.2415 9307.39043 20343 336.2219 415.96840 20373 110.7654 115.41545 20431 27717.1189 16975.48752 50008 550.6863 542.58111 50014 92.1901 80.69506 combinedData <- combine(data, data2) Error in combine(pDataX, pDataY) : data.frames contain conflicting data: non-conforming colname(s): arrayName #--------------------------------------------------------------------- ------ > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8; LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C; LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI ON=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: beadarray affy affyio geneplotter lattice annotate "1.5.14" "1.14.0" "1.4.0" "1.14.0" "0.15-4" "1.14.1" Biobase limma "1.14.0" "2.10.0"

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