Hi, I would like to read thousands of different Affymetrix arrays (HG- U133A, HT_HC-U133A_EA, and HT_HG-U133A). It doesn't seem to automatically detect different arrays and download relevant CDF files. Is there a way to do it with affy package? BW HyunJi

On 11/01/2010 04:56 AM, Hyun Ji wrote: > Hi, > > I would like to read thousands of different Affymetrix arrays (HG- U133A, > HT_HC-U133A_EA, and HT_HG-U133A). It doesn't seem to automatically > detect different arrays and download relevant CDF files. Is there a way > to do it with affy package? I can't tell what you're trying to do. Short reproducible example, sessionInfo please. Maybe ?getCdfInfo Martin > > BW > HyunJi > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Hi HyunJi, On 11/1/2010 7:56 AM, Hyun Ji wrote: > Hi, > > I would like to read thousands of different Affymetrix arrays (HG- U133A, > HT_HC-U133A_EA, and HT_HG-U133A). It doesn't seem to automatically > detect different arrays and download relevant CDF files. Is there a way > to do it with affy package? I'm not sure how the thousands of different arrays comes into the equation (note that you cannot read different chip types into a single AffyBatch), but simply reading the data into an AffyBatch won't result in the download and install of the required CDF. However, doing almost anything else with the AffyBatch will result in that happening. As an example, you can use the show() method: abatch <- ReadAffy() show(abatch) Best, Jim > > BW > HyunJi > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues