Dear Bioconductor list, Does anyone have experience in using Bioconductor for Kinexus antibody arrays? They are spotted arrays with the experiment and control offset from one another. http://www.kinexus.ca/services/kinex/antibody_microarrays.php THANKS! Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "I like it how they tell us that something can either be rational or radical-and this is a college." -Isaac Friedman, age 18

Paul, Thank you very much. That is what I was going to try. I will take you up on your kind offer of the code. Did you use their spot reads or did you read the spots yourself. Best wishes, Rich On Sep 15, 2008, at 7:33 PM, Paul Leo wrote: > > HI Richard , > I have done one of these before using limma. I treated the side-by- > side controls and experimnet as a single "RG" spot (as in a 2 color > array). There is a bit of organizing to get the data in the correct > format, but not too bad. You are welcome to the code if you wish. > Though it will take he a day or two so to clean it up a little. > > Cheers > Paul > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Richard > Friedman > Sent: Sat 9/13/2008 1:54 AM > To: bio c bioconductor > Subject: [BioC] kinexus antibody arrays > > Dear Bioconductor list, > > Does anyone have experience in using Bioconductor for Kinexus > antibody arrays? They are spotted arrays with the experiment and > control > offset from one another. > > http://www.kinexus.ca/services/kinex/antibody_microarrays.php > > THANKS! > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "I like it how they tell us that something can either be rational or > radical-and this is > a college." -Isaac Friedman, age 18 > > _______________________________________________ > 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 >