Hi - I am a Biioconductor neophyte trying to look at data from a 2-channel cDNA microarray that has about 3,000 genes (primarily equine) related to inflammatory and immune response that have been read using ImaGene software. The slides are arranged such that the array is duplicated on the top and bottom half of the slide (ie, the array of genes is printed twice on each slide). Is there somewhere I can read about how to handle such a slide format, beginning with exploratory data analysis (such as basic plots) and normalization? Thank you - Noah Cohen Noah D. Cohen, VMD, MPH, PhD, DACVIM Professor Department of Large Animal Clinical Sciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station, Texas 77843-4475 Telephone: 979-845-3541 Fax: 979-847-8863 e-mail: ncohen at cvm.tamu.edu

Hi Noah,Noah Cohen wrote: > Hi - I am a Biioconductor neophyte trying to look at data from a > 2-channel cDNA microarray that has about 3,000 genes (primarily equine) > related to inflammatory and immune response that have been read using > ImaGene software. The slides are arranged such that the array is > duplicated on the top and bottom half of the slide (ie, the array of > genes is printed twice on each slide). > > Is there somewhere I can read about how to handle such a slide format, > beginning with exploratory data analysis (such as basic plots) and > normalization? I would look at the limma User's Guide. If you have limma installed (likely), then library(limma) limmaUsersGuide() will get you started. Best, Jim > > Thank you - Noah Cohen > > > Noah D. Cohen, VMD, MPH, PhD, DACVIM > Professor > Department of Large Animal Clinical Sciences > College of Veterinary Medicine and Biomedical Sciences > Texas A&M University > College Station, Texas 77843-4475 > Telephone: 979-845-3541 > Fax: 979-847-8863 > e-mail: ncohen at cvm.tamu.edu > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.