Hello, I'm using the affy package for the first time. However, the current version of the affy package doesn't include Affymetrix's MoGene cluster annotation version 2.0. Could you please point out the correct way of re- constructing the annotation packing using the original annotation from the manufacturer's site? For example, the current version throws the following error message: *Produces the following error: * *background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain MoGene-2_0-st Library - package mogene20stcdf not installed Bioconductor - mogene20stcdf not available* I'd appreciate any help and thank you for your time. Best, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Mon, Jan 21, 2013 at 8:00 AM, Rafael Irizarry <rairizarry@gmail.com>wrote: > Paul, Please send this to the Bioconductor mailing list > > On Sun, Jan 20, 2013 at 3:11 PM, Paul Rigor <paul.rigor@uci.edu> wrote: > > Hello, > > I'm using the affy package for the first time. However, the current > version > > of the affy package doesn't include Affymetrix's MoGene cluster > annotation > > version 2.0. Could you please point out the correct way of > re-constructing > > the annotation packing using the original annotation from the > manufacturer's > > site? For example, the current version throws the following error > message: > > > > Produces the following error: > > > > background correction: mas > > PM/MM correction : mas > > expression values: mas > > background correcting...Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain MoGene-2_0-st > > Library - package mogene20stcdf not installed > > Bioconductor - mogene20stcdf not available > > > > > > I'd appreciate any help and thank you for your time. > > > > Best, > > Paul > > > > -- > > Paul Rigor > > http://www.ics.uci.edu/~prigor > [[alternative HTML version deleted]]

Hi Paul, I would recommend switching to either the oligo or xps package for analyzing these data. The affy package was never intended to be used with the random primer Affy arrays, whereas oligo and xps are. Best, Jim On 1/21/2013 5:13 PM, Paul Rigor wrote: > Hello, > I'm using the affy package for the first time. However, the current version > of the affy package doesn't include Affymetrix's MoGene cluster annotation > version 2.0. Could you please point out the correct way of re- constructing > the annotation packing using the original annotation from the > manufacturer's site? For example, the current version throws the following > error message: > > *Produces the following error: > > * > *background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-2_0-st > Library - package mogene20stcdf not installed > Bioconductor - mogene20stcdf not available* > > > I'd appreciate any help and thank you for your time. > > Best, > Paul > > > -- > Paul Rigor > http://www.ics.uci.edu/~prigor > > > On Mon, Jan 21, 2013 at 8:00 AM, Rafael Irizarry<rairizarry at="" gmail.com="">wrote: > >> Paul, Please send this to the Bioconductor mailing list >> >> On Sun, Jan 20, 2013 at 3:11 PM, Paul Rigor<paul.rigor at="" uci.edu=""> wrote: >>> Hello, >>> I'm using the affy package for the first time. However, the current >> version >>> of the affy package doesn't include Affymetrix's MoGene cluster >> annotation >>> version 2.0. Could you please point out the correct way of >> re-constructing >>> the annotation packing using the original annotation from the >> manufacturer's >>> site? For example, the current version throws the following error >> message: >>> Produces the following error: >>> >>> background correction: mas >>> PM/MM correction : mas >>> expression values: mas >>> background correcting...Error in getCdfInfo(object) : >>> Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain MoGene-2_0-st >>> Library - package mogene20stcdf not installed >>> Bioconductor - mogene20stcdf not available >>> >>> >>> I'd appreciate any help and thank you for your time. >>> >>> Best, >>> Paul >>> >>> -- >>> Paul Rigor >>> http://www.ics.uci.edu/~prigor > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099