Hi, I am trying to summarize and normalize Human Affymetrix data using the Bioconductor library "affy" and the "bg.correct" method, like I usually do with other datasets (recently done on Mouse data). But I get this error about the cdf environment: --- # Load libraries > library("affy") > library("affyPLM") # List cel files > list.celfiles() # Read in cel files > DataRaw <- ReadAffy() > probes.bg.rma <- bg.correct(DataRaw, method = "rma") Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available --- I found some discussions on this mailing list about this issue so I tried to fix it by installing the "hugene10stv1.r3cdf" package. But I got a warning and then still the same error when calling "bg.correct": --- > source("http://bioconductor.org/biocLite.R") > biocLite("hugene10stv1.r3cdf") Using R version 2.9.2, biocinstall version 2.4.13. Installing Bioconductor version 2.4 packages: [1] "hugene10stv1.r3cdf" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘hugene10stv1.r3cdf’ is not available > probes.bg.rma <- bg.correct(DataRaw, method = "rma") Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available --- I also tried to give the cdf filename to the "ReadAffy" function but still the same error : --- > source("http://bioconductor.org/biocLite.R") > biocLite("hugene10stv1.r3cdf") #same warning # Use ReadAffy with the CDF file name > DataRaw<- ReadAffy(cdfname = "hugene10stv1.r3cdf") > probes.bg.rma <- bg.correct(DataRaw, method = "rma") Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hugene10stv1.r3cdf Library - package hugene10stv1.r3cdf not installed Bioconductor - hugene10stv1.r3cdf not available # Try to get information about the cdf environment: > getCdfInfo(DataRaw) Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 Error in getCdfInfo(DataRaw) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hugene10stv1.r3cdf Library - package hugene10stv1.r3cdf not installed Bioconductor - hugene10stv1.r3cdf not available --- Please let me know what I possibly did wrong and how to fix this cdf environment issue. Many thanks for your time and comprehension. Best regards, Roxane LEGAIE Bioinformatician -- Warwick Systems Biology Centre Coventry House University of Warwick Coventry CV4 7AL U.K. +44 (0)24 761 50332 R.Legaie@warwick.ac.uk http://www2.warwick.ac.uk/fac/sci/systemsbiology/ [[alternative HTML version deleted]]

Hi Roxane, You don't mention your OS. Are you perhaps using MacOS X 10.5 (or 10.6)? If so, you can see that the package binary isn't available for that version, which may be the problem you are encountering. If you are set up to build packages (see here if not: http://r.research.att.com/tools/ I believe all you need are the Xcode Development tools.), then you can simply do biocLite("hugene10stv1.r3cdf", type = "source") Best, Jim Legaie, Roxane wrote: > Hi, > I am trying to summarize and normalize Human Affymetrix data using the Bioconductor library "affy" and the "bg.correct" method, like I usually do with other datasets (recently done on Mouse data). > But I get this error about the cdf environment: > > --- > # Load libraries >> library("affy") >> library("affyPLM") > # List cel files >> list.celfiles() > # Read in cel files >> DataRaw <- ReadAffy() >> probes.bg.rma <- bg.correct(DataRaw, method = "rma") > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > --- > > > I found some discussions on this mailing list about this issue so I tried to fix it by installing the "hugene10stv1.r3cdf" package. > But I got a warning and then still the same error when calling "bg.correct": > > --- >> source("http://bioconductor.org/biocLite.R") >> biocLite("hugene10stv1.r3cdf") > Using R version 2.9.2, biocinstall version 2.4.13. > Installing Bioconductor version 2.4 packages: > [1] "hugene10stv1.r3cdf" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?hugene10stv1.r3cdf? is not available > >> probes.bg.rma <- bg.correct(DataRaw, method = "rma") > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > --- > > > I also tried to give the cdf filename to the "ReadAffy" function but still the same error : > --- >> source("http://bioconductor.org/biocLite.R") >> biocLite("hugene10stv1.r3cdf") > #same warning > # Use ReadAffy with the CDF file name >> DataRaw<- ReadAffy(cdfname = "hugene10stv1.r3cdf") >> probes.bg.rma <- bg.correct(DataRaw, method = "rma") > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hugene10stv1.r3cdf > Library - package hugene10stv1.r3cdf not installed > Bioconductor - hugene10stv1.r3cdf not available > > # Try to get information about the cdf environment: >> getCdfInfo(DataRaw) > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > Error in getCdfInfo(DataRaw) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hugene10stv1.r3cdf > Library - package hugene10stv1.r3cdf not installed > Bioconductor - hugene10stv1.r3cdf not available > --- > > > Please let me know what I possibly did wrong and how to fix this cdf environment issue. > > Many thanks for your time and comprehension. > Best regards, > > Roxane LEGAIE > Bioinformatician > -- > Warwick Systems Biology Centre > Coventry House > University of Warwick > Coventry CV4 7AL > U.K. > +44 (0)24 761 50332 > R.Legaie at warwick.ac.uk > http://www2.warwick.ac.uk/fac/sci/systemsbiology/ > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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