OOPS - so sorry, but I made a mistake in copying the script of my previous email. Here is the correct version: Could someone please spot the error that I am making in creating a cdf environment? > library(affy) > library(makecdfenv) > pname<-cleancdfname(whatcdf("YY002001.cel")) > list(pname) [[1]] [1] "xxxx007a46cdf" > xxxx007a46cdf<-make.cdf.env("xxxx007a46.cdf") Reading CDF file. Creating CDF environment Wait for about 827 dots....... > length(ls(xxxx007a46cdf)) [1] 82661 > eset<-justRMA() Note: Using download type: Win32 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment specified did not contain XXXX007a46 Library - package xxxx007a46cdf not installed Data for package affy did not contain XXXX007a46 Bioconductor - xxxx007a46cdf not available Thanks for your help, again. C. Hannam

It seems you didn't create/install the CDF package. ?make.cdf.package b. On Wed, 31 Aug 2005, Carol Hannam wrote: > Library - package xxxx007a46cdf not installed > Thanks for your help, again. > C. Hannam

Carol Hannam wrote: > OOPS - so sorry, but I made a mistake in copying the script of my previous > email. Here is the correct version: > > > Could someone please spot the error that I am making in creating a cdf > environment? > > >>library(affy) >>library(makecdfenv) >>pname<-cleancdfname(whatcdf("YY002001.cel")) >>list(pname) > > [[1]] > [1] "xxxx007a46cdf" There appears to be an oversight in the function getCdfInfo(). If you are using make.cdf.env(), you should name your env XXXX007a46 rather than using the cleancdfname. So basically change the line below to read XXXX007a46 <- make.cdf.env("xxxx007a46.cdf") and it should work for you. NB: Note the error message below - although rather cryptic, it does state that it couldn't find the environment XXXX007a46, which was a subtle hint in the right direction. Best, Jim > > >>xxxx007a46cdf<-make.cdf.env("xxxx007a46.cdf") > > Reading CDF file. > Creating CDF environment > Wait for about 827 dots....... > >>length(ls(xxxx007a46cdf)) > > [1] 82661 > >>eset<-justRMA() > > Note: Using download type: Win32 > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment specified did not contain XXXX007a46 > Library - package xxxx007a46cdf not installed > Data for package affy did not contain XXXX007a46 > Bioconductor - xxxx007a46cdf not available > > Thanks for your help, again. > C. Hannam > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623