I am new to R. I have bead chip data from several chips. I am following Beadarray package and followed the commands from the beadarrayExampleData (Analysis of Bead-summary Data using beadarray, Mark Dunning, November 9, 2011). These commands work good for my chip data but I get stuck after "channelNames(BSData)" which returns "[1] "G"" but after that when I use the next command "BSData.log2 <- channel(BSData, "G")", I get the error message "Error in object@channelData[[2]] : subscript out of bounds" and I can not go further with Exploratory analysis using boxplots. The following commands work: randIDs <- sample(featureNames(BSData), 1000) BSData[randIDs, ] But after that when I go to next command "boxplot(BSData.log2[randIDs, ])" or any subsequent command, I get error messages "Error in boxplot(BSData.log2[randIDs, ]) :   error in evaluating the argument 'x' in selecting a method for function 'boxplot': Error: object 'BSData.log2' not found". Can anyone help me with this please. I have wasted a lot of time getting over this problem but I cant. Please help me. Thanks. Cuteguy Following is session info: R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.4.1 ggplot2_0.9.0 Biobase_2.14.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.16.11 colorspace_1.2-0 DBI_0.2-5 [4] dichromat_1.2-4 digest_0.5.1 grid_2.14.2 [7] IRanges_1.12.5 limma_3.10.2 MASS_7.3-17 [10] memoise_0.1 munsell_0.3 plyr_1.7.1 [13] proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 [16] RSQLite_0.11.1 scales_0.2.0 stringr_0.6 [[alternative HTML version deleted]]