Hey all, I have been following the BeadSummary tutorial for beadarray and when i get to the step where i filter out the probes that have a quality of "Bad" and "No Match" ids <- as.character(featureNames(BSData.norm)) qual <- unlist(mget(ids, illuminaHumanv4PROBEQUALITY, ifnotfound = NA)) table(qual) Bad Good Good*** Good**** No match Perfect 12376 1158 137 507 468 27335 Perfect*** Perfect**** 2911 2394 rem <- qual == "No match" | qual == "Bad" | is.na(qual) BSData.filt <- BSData.norm[!rem, ] I get the following error Error in FUN(X[[2L]], ...) : (subscript) logical subscript too long I was wondering if any one can help me figure out what's going on or help me come up with an alternative to filter out the reads with poor probe quality Thanks in advance Will -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv4.db_1.14.0 org.Hs.eg.db_2.7.1 [3] RSQLite_0.11.1 DBI_0.2-5 [5] AnnotationDbi_1.18.1 beadarray_2.6.0 [7] ggplot2_0.9.1 Biobase_2.16.0 [9] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] BeadDataPackR_1.8.0 colorspace_1.1-1 dichromat_1.2-4 [4] digest_0.5.2 grid_2.15.1 IRanges_1.14.4 [7] labeling_0.1 limma_3.12.1 MASS_7.3-18 [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] scales_0.2.1 stats4_2.15.1 stringr_0.6.1 [19] tools_2.15.1 > -- Sent via the guest posting facility at bioconductor.org.