Dear all, I have installed illuminaMousev2BeadID.bd in order to re annotate my differentially expressed gene list (annotated with manufacturer annotation) according to Illumina MouseWGv2 annotation data. I am rather confused with the procedure as I have never dealt with annotation packages before. What I have is a data frame with probeID, IlluminaProbeIds....see test.txt file) and I want to get rid of all bad data as defined from http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) . I guess this annotation package contains only the "good"information and I would like to use this to clean my txt file and I am not sure where to start. Thanks in advance for any pointers/scripts. Nathalie > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaMousev2BeadID.db_1.6.1 org.Mm.eg.db_2.4.1 [3] RSQLite_0.9-1 DBI_0.2-5 [5] AnnotationDbi_1.10.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] tools_2.11.1 -- 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. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20110919="" b16bce44="" attachment.txt="">