My question is the following: I have Affymetrix SNP 6.0 chip data loaded in R as ExpressionSet object: ExpressionSet (storageMode: lockedEnvironment) assayData: 18538 features, 1001 samples I need to annotate them to get list specifying the metadata annotation of the chromosome location on the genome, list specifying the metadata annotation of the location of the probe on the chromosome and list specifying the metadata annotation of the symbol corresponding to the probe. I will use this data for further analysis with SIM package. All these data should be loaded in R as ProbeAnnDbBimap object. But it seems there is no library like illuminaHumanv3.db but for AffymetrixSNP6.0 Thanks much, Svetlana -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] pd.genomewidesnp.6_1.8.0 oligo_1.22.0 oligoClasses_1.20.0 [4] RSQLite_0.11.2 DBI_0.2-5 BiocInstaller_1.8.3 [7] missForest_1.3 randomForest_4.6-7 rms_3.6-0 [10] Hmisc_3.10-1 MASS_7.3-22 BCC_1.0-9 [13] sessionTools_0.9-2 synapseClient_0.18-0 predictiveModeling_0.12-5 [16] randomSurvivalForest_3.6.3 glmnet_1.8-2 Matrix_1.0-10 [19] survcomp_1.8.1 prodlim_1.3.2 KernSmooth_2.23-8 [22] survival_2.36-14 affy_1.36.0 caret_5.15-044 [25] cluster_1.14.3 reshape_0.8.4 plyr_1.7.1 [28] lattice_0.20-10 foreach_1.4.0 Biobase_2.18.0 [31] BiocGenerics_0.4.0 limma_3.14.1 loaded via a namespace (and not attached): [1] Biostrings_2.26.2 GenomicRanges_1.10.5 IRanges_1.16.3 RCurl_1.95-1.1 [5] RJSONIO_1.0-1 SuppDists_1.1-8 affxparser_1.30.0 affyio_1.26.0 [9] bit_1.1-9 bootstrap_2012.04-0 codetools_0.2-8 digest_0.5.2 [13] ff_2.2-10 grid_2.15.1 iterators_1.0.6 parallel_2.15.1 [17] preprocessCore_1.20.0 rJava_0.9-3 rmeta_2.16 stats4_2.15.1 [21] survivalROC_1.0.0 tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.