Hi all I am working with affy's human GeneSete 1.0 ST. I download hugene10st.db annotation database but that was the only package I found. When I try to do rma or gcmra it gives me teh following error. So it is looking for the CDF environment for this chip. Aren't those ready yet?? any help will be appreciated. Tx, mayte Warning: unable to access index for repository http:// brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.8 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 [[alternative HTML version deleted]]

Hi Mayte, http://www.bioconductor.org/docs/workflows/oligoarrays/ Best, Jim Mayte Suarez-Farinas wrote: > Hi all > > I am working with affy's human GeneSete 1.0 ST. I download > hugene10st.db annotation database but > that was the only package I found. When I try to do rma or gcmra it > gives me teh following error. > So it is looking for the CDF environment for this chip. Aren't those > ready yet?? > any help will be appreciated. > Tx, mayte > > > Warning: unable to access index for repository http:// > brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.8 > 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 > > > [[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 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Hi Mayte, if you call rma from the oligo package you only need a pdInfoPackage that you can either build yourself or download (I built it quite some time ago to be found here: http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) best T. On Mar 27, 2009, at 4:12 PM, Mayte Suarez-Farinas wrote: > Hi all > > I am working with affy's human GeneSete 1.0 ST. I download > hugene10st.db annotation database but > that was the only package I found. When I try to do rma or gcmra it > gives me teh following error. > So it is looking for the CDF environment for this chip. Aren't those > ready yet?? > any help will be appreciated. > Tx, mayte > > > Warning: unable to access index for repository http:// > brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.8 > 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 > > > [[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 ---------------------------------------------------------------------- Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D