Hello, I am using soychip data for R which unlike human etc is not publicly available so it is not available in the metadata on bioconductor. > > I have it on my desktop, sent directly from affy. > Being on the desktop, I thought that meant the cdf files were available, BUT > When I am attempting to read the data for the soybean file, I type in eset <- rma (Data) and the error reads this: > ?Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: > Specified environment specified did not contain Soybean > Library - package soybeancdf not installed > Data for package affy did not contain Soybean > Bioconductor - soybeancdf not available? > > The soybeancdf has been installed into the affy library but it is not on Bioconductor?s website of packages available to download. Is this why it will not open? > > Any suggestions as to what I should do to rectify this problem? Thank you. Joyce Curry Virginia Bioinformatics Institute, Virginia Tech Bioinformatics 1 Washington Street Blacksburg, VA 24061-0447

You have to convert your soybean cdf to a cdfenv in order for affy to be able to use it. The function to do this can be found in the makecdfenv package on BioC, specifically make.cdf.env() and make.cdf.package(). The former will make a cdfenv that you can use (and save) as an environment, and the latter will make a package that will have to be installed before you can use it (much like the packages available on the metadata page of BioC). If you have problems making the cdfenv, you could send the cdf to me (zipped of course) and I will make the package for you. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <jcurry@vbi.vt.edu> 07/21/04 02:57PM >>> Hello, I am using soychip data for R which unlike human etc is not publicly available so it is not available in the metadata on bioconductor. > > I have it on my desktop, sent directly from affy. > Being on the desktop, I thought that meant the cdf files were available, BUT > When I am attempting to read the data for the soybean file, I type in eset <- rma (Data) and the error reads this: > "Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: > Specified environment specified did not contain Soybean > Library - package soybeancdf not installed > Data for package affy did not contain Soybean > Bioconductor - soybeancdf not available" > > The soybeancdf has been installed into the affy library but it is not on Bioconductor's website of packages available to download. Is this why it will not open? > > Any suggestions as to what I should do to rectify this problem? Thank you. Joyce Curry Virginia Bioinformatics Institute, Virginia Tech Bioinformatics 1 Washington Street Blacksburg, VA 24061-0447 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor