I am having trouble reading a human exon array chip using the affylmGUI software. The program cannot find the HuEx-l_OST-V2 file, although I have it downloaded. I am a new user to R and microarrays in general. Please let me know if there is anyway to use the software with the Human exon array. Matt Walker mattw at uchicago.edu University of Chicago Geof Greene Lab

Hi Matt, Matthew Walker wrote: > I am having trouble reading a human exon array chip using the > affylmGUI software. The program cannot find the HuEx-l_OST-V2 file, > although I have it downloaded. I am a new user to R and microarrays > in general. Please let me know if there is anyway to use the software > with the Human exon array. The affylmGUI software is not designed to work directly with the raw exon chip data. Your closest bet would be to use the oligo package. However, the oligo package is still under development so is probably not the best place for a new R user to start. In addition, the oligo package will require you to make a PDEnv with the HuEx-l_OST-V2.cdf file, which I am unable to do on a 64 bit Linux box with 8 Gb RAM (I think 16 Gb is sufficient). Probably your best bet would be to get Affy's Exact software and use that to compute expression values for each probeset (exon), and then import those data into R. This will still require a reasonably large amount of RAM, and will likely be easier to do on a *nix variant (you don't mention your OS). Other options would include buying some commercial software like Genomatix or XRAY, etc. See here for some choices: http://www.affymetrix.com/products/software/compatible/exon_expression .affx Best, Jim > > Matt Walker > mattw at uchicago.edu > University of Chicago > Geof Greene Lab > > _______________________________________________ > 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.