Hi. I'm working with bioconductor since 2 month and I never had any problems. I used CEL-Files from ATGenExpress and everything was okay. Now I tried to analyse different CEL-Files of yeast. I used different sources ( http://chemogenomics.stanford.edu/supplements/01yfh/files/raw_data/tar _archives/ http://www.brownlab.info/publications/Brown2005/celfiles/index.htm ) But I didn't succeeded to make an library(affy) and than data <- justRMA() in the cel-file directory. On two different machines I got two different errors. The first computer says: ########################## > data <- justRMA() Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain DNA_TAGS_3 Library - package dnatags3cdf not installed Data for package affy did not contain dnatags3cdf Bioconductor - dnatags3cdf not available ########################## and the second one says: ########################## library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools > data <- justRMA() Note: BIOCRel1.8/src/contrib does not seem to have a valid repository, skipping Warning: Failed to read replisting at BIOCRel1.8/src/contrib in: getReplisting(repURL, repFile, method = method) Note: BIOCRel1.8/bin/windows/contrib/2.3 does not seem to have a valid repository, skipping Warning: 1: Failed to read replisting at BIOCRel1.8/bin/windows/contrib/2.3 in: getReplisting(repURL, repFile, method = method) 2: Failed opening: HTTP Status war '404 Not Found' Note: http://www.bioconductor.org/packages/data/annotation/stable/bin/window s/contrib/2.3 does not seem to have a valid repository, skipping Note: Using download type: Source Fehler in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment specified did not contain DNA_TAGS_3 Library - package dnatags3cdf not installed Data for package affy did not contain DNA_TAGS_3 Bioconductor - dnatags3cdf not available Warning: Failed to read replisting at http://www.bioconductor.org/packages/data/annotation/stable/bin/window s/contrib/2.3 in: getReplisting(repURL, repFile, method = method) ############################## Maybe anyone had the same problem allready and can help me out of this. Thanks in advance. Best regards. Roman Brunnemann

Hi Roman, Roman Brunnemann wrote: > Hi. > > I'm working with bioconductor since 2 month and I never had any > problems. I used CEL-Files from ATGenExpress and everything was okay. > Now I tried to analyse different CEL-Files of yeast. I used > different sources ( > > http://chemogenomics.stanford.edu/supplements/01yfh/files/raw_data/t ar_archives/ > http://www.brownlab.info/publications/Brown2005/celfiles/index.htm ) > > > But I didn't succeeded to make an > > library(affy) and than data <- justRMA() in the cel-file directory. > On two different machines I got two different errors. The first > computer says: > > ########################## > > >> data <- justRMA() > > Error in getCdfInfo(object) : Could not obtain CDF environment, > problems encountered: Specified environment does not contain > DNA_TAGS_3 Library - package dnatags3cdf not installed Data for > package affy did not contain dnatags3cdf Bioconductor - dnatags3cdf > not available The problem here is that you need the DNA_TAGS_3.CDF file in order to analyze these data. BioConductor only makes available those CDF files that are publicly available from Affy's website, and unfortunately this isn't one of them. In order to analyze these data, you will need to do two things; first, you will need to find the DNA_TAG_3.CDF file (maybe you can get it from the Brown lab?), and second, you will need to build either a cdfenv or a cdf package using the makecdfenv package. See ?make.cdf.env for more information. Best, Jim -- 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