Hi Roy, In our group we have been developed the beadarray R package for the analysis of Illumina BeadArrays. It is able to read both the output from Illumina's BeadStudio or the raw data if you have access to it. The objects it creates are very similar in style to limma and affy and it is also very easy to convert to ExpressionSet object types. The package is available as part of the 1.8 release of Bioconductor (http://bioconductor.org/packages/1.8/bioc/html/beadarray.html). There is also a version in the developers section which we are adding to all the time (recently we made significant improvements in the time taken to process bead level data). Please let me know if you have any further questions. Regards, Mark -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Roy Williams Sent: 25 May 2006 06:29 To: bioconductor at stat.math.ethz.ch Subject: [BioC] LimmaGUI for illumina data Hi, I have 2 questions: 1. I would be really grateful to have a list of papers that cite limma - does such a list exist? If so could someone send it to me. 2. I would like to use the limmaGUI or AffyLMGUI package with illumina array data www.illumina.com). Is this possible? Could I load a .RData (or .lmn) data object which has just the column headers (experiments) and gene names along with the data? I have been using limma from the command line and it would help considerably to have a GUI which prints HTML reports. Many thanks for any advice you might be able to offer, Roy -- Roy Williams PhD The Burnham Institute for Medical Research Bioinformatics Shared Resource Building 10 Offices 2405/6 3010 Science Park Road San Diego, California 92121 USA Tel: 858 646 3100 ext 3915 email: royw at burnham.org web site: idmweb.burnham.org _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor