Hi Will, It looks as though you are using the Illumina Humanv4 package to do your annotation, whereas the example code was written with the Humanv3 annotation. Are you trying to follow the vignette with your own data? What is the length of the 'rem' vector and the dimensions of the BSData.norm object? There might be some mismatch here; > length(rem) [1] 49576 > dim(exampleSummaryData.norm) Features Samples Channels 49576 12 1 Regards, Mark On Sun, Aug 26, 2012 at 8:21 PM, Will [guest] <guest at="" bioconductor.org=""> wrote: > > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor