I am very new to R and bioconductor, I assume this is obscure but easy. I have CEL fils from a custom Affymetrix array. I also have a CDF. I have imported the cel files using abatch <- ReadAffy(celfile.path='/Users/vmd/Dropbox/dna/data/Raw_Data_CEL_Zip/Ty pe_1') then trying to use fitPLM() Pset <- fitPLM(abatch) I get this error: Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .10 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Tgondiia520372 Library - package tgondiia520372cdf not installed Bioconductor - tgondiia520372cdf not available I have the CDF file but am unsure how to instruct fitPLM to reference it? *Vincent Davis 720-301-3003 * vincent@vincentdavis.net my blog <http: vincentdavis.net=""> | LinkedIn<http: www.linkedin.com="" in="" vincentdavis=""> [[alternative HTML version deleted]]

Hi Vincent, Vincent Davis wrote: > I am very new to R and bioconductor, I assume this is obscure but easy. I > have CEL fils from a custom Affymetrix array. I also have a CDF. > I have imported the cel files using > abatch <- > ReadAffy(celfile.path='/Users/vmd/Dropbox/dna/data/Raw_Data_CEL_Zip/ Type_1') > then trying to use fitPLM() > Pset <- fitPLM(abatch) > I get this error: > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.10 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain Tgondiia520372 > Library - package tgondiia520372cdf not installed > Bioconductor - tgondiia520372cdf not available > > I have the CDF file but am unsure how to instruct fitPLM to reference it? You need to use the makecdfenv package. There is a vignette that comes with the package that shows how to create and install the package. Best, Jim > > > *Vincent Davis > 720-301-3003 * > vincent at vincentdavis.net > my blog <http: vincentdavis.net=""> | > LinkedIn<http: www.linkedin.com="" in="" vincentdavis=""> > > [[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