Hello all, There have been some posts regarding switching to the new "lumi____All.db" annotation packages. The problem is, if you have "older" BeadStudio output the probe sequence is not in the files, so the these packages cannot be initially used: lumiR("test_sample_gene_profile.txt", lib="lumiMouseAll.db") Warning messages: 1: In addNuId2lumi(x.lumi, lib = lib) : lumiMouseAll.db does not include nuID conversion information! 2: In addNuId2lumi(x.lumi, lib = lib) : Please provide the annotation file or lumi annotation library! So, you can either download and specify an Illumina provided csv file with the probe/target sequence information, or use the older packages (version matched): lumiR("test_sample_gene_profile.txt", lib="lumiMouseV1") I happen to have many files from this version of BeadStudio, so this last option seems like a very practical solution to get into the nuID space... (but you have to install this "old" package) Any comments or suggestions would be greatly appreciated... Cheers, Cei sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] lumiMouseV1_1.3.1 lumiMouseAll.db_1.2.0 AnnotationDbi_1.2.0 [4] RSQLite_0.6-8 DBI_0.2-4 lumi_1.6.0 [7] mgcv_1.3-30 affy_1.18.0 preprocessCore_1.2.0 [10] affyio_1.8.0 Biobase_2.0.0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.