Help on Illumina HumanHT12 v4 chromosome filtering
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Kemal Akat ▴ 120
Last seen 7.9 years ago
Hi all, I am running into problems when I want to remove probes targeting chromosome Y. I can reproduce this behavior with the data from the beadarrayExampleData package: library(beadarray) library(illuminaHumanv4.db) library(beadarrayExampleData) data(exampleSummaryData) ## filter for probe quality ids = as.character(featureNames(exampleSummaryData)) qual = unlist(mget(ids, illuminaHumanv4PROBEQUALITY, ifnotfound = NA)) rem = qual == "No match" | qual == "Bad" | exampleSummaryData_filt = exampleSummaryData[!rem] ## get chromosome location for remaining probes ids = as.character(featureNames(exampleSummaryData_filt)) chr = unlist(mget(ids, illuminaHumanv4CHR, ifnotfound = NA)) ## filter out probes targeting the Y chromosome rem_chr= chr == "Y" exampleSummaryData_filt = exampleSummaryData_filt[!rem_chr] Error in obj[i, , ..., drop = drop] : (subscript) logical subscript too long Calls: [ ... [ -> callNextMethod -> .nextMethod -> lapply -> FUN The eSet (Illumina) object starts with R> dim(exampleSummaryData) Features Samples Channels 49576 12 2 probes. After quality filtering R> dim(exampleSummaryData_filt) ## after filtering for probe quality Features Samples Channels 30084 12 2 R> Now, for the second filtering (ids = as.character(featureNames(exampleSummaryData_filt) etc.): R> length(ids) [1] 30084 R> length(chr) [1] 30109 Where are the extra probes coming from? I tried to match only the ones in exampleSummaryData_filt), idx = match(ids, names(chr)) chr = chr[idx] but this led to other problems. Maybe I am missing something obvious? Thank you for any hints or help! Kemal R> sessionInfo() R Under development (unstable) (2013-02-06 r61857) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] beadarrayExampleData_1.0.5 illuminaHumanv4.db_1.16.0 RSQLite_0.11.2 [5] DBI_0.2-5 AnnotationDbi_1.21.13 beadarray_2.9.2 ggplot2_0.9.3 [9] Biobase_2.19.3 BiocGenerics_0.5.6 setwidth_1.0-1 loaded via a namespace (and not attached): [1] AnnotationForge_1.1.10 BeadDataPackR_1.11.0 colorspace_1.2-0 dichromat_1.2-4 digest_0.6.0 [6] grid_3.0.0 gtable_0.1.2 IRanges_1.17.36 labeling_0.1 limma_3.15.15 [11] MASS_7.3-23 munsell_0.4 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 [16] reshape2_1.2.2 scales_0.2.3 stats4_3.0.0 stringr_0.6.2 tools_3.0.0 R>
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