Hello, I am using the re-annotation of Illumina probe sequences available in the IlluminaMousev2.db (great package!), and I have two questions (please see code below as well): 1) Is there any difference between Good and Good*** or Perfect and Perfect**** probe quality? 2) I noticed there are two probes re-annotated to an EntrezID without probe quality, why would this be? Thanks! Lourdes > library("illuminaMousev2.db") > x <- illuminaMousev2ENTREZREANNOTATED > mapped_probes <- mappedkeys(x) > xx <- as.list(x[mapped_probes]) > probe_EntrezID_re <- unlist(xx) > > x <- illuminaMousev2PROBEQUALITY > mapped_probes <- mappedkeys(x) > # Convert to a list > xx <- as.list(x[mapped_probes]) > probe_quality_re <- unlist(xx) > > table(probe_quality_re[intersect(names(probe_EntrezID_re), names(probe_quality_re))]) Bad Good Good*** Good**** No match Perfect Perfect*** Perfect**** 3657 996 38 302 79 31819 1719 1047 > > setdiff(names(probe_EntrezID_re), names(probe_quality_re)) [1] "ILMN_1229593" "ILMN_2694153" > probe_quality_re[c("ILMN_1229593", "ILMN_2694153")] <na> <na> NA NA > > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 bitops_1.0-4.1 [5] gdata_2.8.2 gtools_2.6.2 limma_3.10.2 illuminaMousev2.db_1.12.1 [9] org.Mm.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.15 [13] Biobase_2.14.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] IRanges_1.12.6 tools_2.14.1 [[alternative HTML version deleted]]