Our core has produced raw lumi output for me that includes these annotation columns: [51] "SEARCH_KEY" "UNIGENE_ID" [53] "ENTREZ_GENE_ID" "ACCESSION" [55] "SYMBOL" "PROBE_ID" [57] "DEFINITION" "X" lumiR reads the following annotation columns: ACCESSION, SYMBOL, PROBE START, CHROMOSOME, PROBE CHR ORIENTATION, PROBE COORDINATES, DEFINITION. Perhaps since these are not there, I get this message: Please provide the annotation file or lumi annotation library! What is unclear to me, having read the lumi documentation, is whether I can avoid this message by just adding bioconductor annotations in. I tried it like this > data <- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping") Warning message: In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : More than 500 identifiers cannot be found in the library:lumiHumanIDMapping! The provided library might be wrong or outdated! > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumiHumanIDMapping_1.8.0 RSQLite_0.9-4 DBI_0.2-5 [4] AnnotationDbi_1.12.0 lumi_2.2.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 [4] grid_2.12.0 hdrcde_2.15 KernSmooth_2.23-4 [7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44 [10] methylumi_1.6.1 mgcv_1.6-2 nlme_3.1-97 [13] preprocessCore_1.12.0 tcltk_2.12.0 xtable_1.5-6 [[alternative HTML version deleted]]