Hello, just wanted to report this: If you're processing a single illumina array, and using beadarray's calculateDetection, you get an error: Error in negControls[, i] : incorrect number of dimensions This appears to be due to the default drop to lower dimension, in this line (in beadarray:::getNegatives): nData = exprs(BSData)[nIDs, ] which should be: nData = exprs(BSData)[nIDs, ,drop=FALSE] Cheers, Cei > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 [4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [7] AnnotationDbi_1.4.2 lattice_0.17-20 limma_2.16.3 [10] Biobase_2.2.1 loaded via a namespace (and not attached): [1] DBI_0.2-4 KernSmooth_2.22-22 RColorBrewer_1.0-2 RSQLite_0.7-1 [5] grid_2.8.0