I just got a new 12 plex chip to look at. To my eye, the data structure of the new file, called FinalReport.txt looks just like the old 8 plex version, but the old data loads up fine while the new data has some issue, complaining: Please provide the annotation file or lumi annotation library! Any ideas? Best, Tom > sessionInfo() R version 2.10.1 (2009-12-14) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.12.4 MASS_7.3-4 RSQLite_0.8-0 [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 [7] affy_1.24.2 annotate_1.24.0 AnnotationDbi_1.8.1 [10] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26 Matrix_0.999375-33 [5] nlme_3.1-96 tools_2.10.1 xtable_1.5-6

Hi, Tom Your lumi is out of date, right now it is 2.2.0. So you have to upgrade your R and BioC to the latest ones so that you can use lumi and annotation files if you want to use bioClite to install these packages, or you have to do that manually. Thanks Gilbert On 12/15/10 2:18 PM, Thomas Hampton wrote: > I just got a new 12 plex chip to look at. To my eye, the data structure > of the new file, > called FinalReport.txt looks just like the old 8 plex version, but the > old data loads > up fine while the new data has some issue, complaining: > > Please provide the annotation file or lumi annotation library! > > > Any ideas? > > Best, > > Tom > > > sessionInfo() > R version 2.10.1 (2009-12-14) > i386-apple-darwin8.11.1 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_1.12.4 MASS_7.3-4 RSQLite_0.8-0 > [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 > [7] affy_1.24.2 annotate_1.24.0 AnnotationDbi_1.8.1 > [10] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26 Matrix_0.999375-33 > [5] nlme_3.1-96 tools_2.10.1 xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- ----------------------------------------------- Gang (Gilbert) Feng, PhD Biomedical Informatics Center Robert H. Lurie Comprehensive Cancer Center Northwestern University 750 N. Lake Shore Drive, 11th Floor(11-175e) Chicago, IL 60611 Phone:312-503-2358 Email g-feng (at) northwestern.edu