Good morning, Sorry to trouble the list. My overall goal is to obtain a normalized data set.I would like to do it using a custom cdf. hs133phsentrezgcdf. I am using R 2.9.0 on SUSE Linux 10.1. (newbie to Linux, would prefer to use Windows, but it can't manage the memory requirements for 150 HGU133Plus2.0 CEL files). I have installed the cdf in Windows without problems, I just moved it to the library directory there. I am however struggling over installation of this cdf in Linux. In terms of directories, to install R, have done ./configure --prefix=/usr/bin/R/2.9.0 make su make install exit() R -> /usr/bin/R/2.9.0/bin/R I suspect there are permission issues, as I get these warning messages in R. > install.packages("survival") Warning in install.packages("survival") : argument 'lib' is missing: using '/home/minhan/R/x86_64-unknown-linux-gnu-library/2.9' However, there are no issues installing packages otherwise, and they seem to work fine. I have downloaded the CDF hs133phsentrezgcdf version 10, tar xvf done, and moved the directory to /home/minhan/R/x86_64-unknown-linux-gnu-library/2.9 However, I get this error. > library(hs133phsentrezgcdf) Error in library(hs133phsentrezgcdf) : 'hs133phsentrezgcdf' is not a valid installed package Ideally, I would like to do source("http://bioconductor.org/biocLite.R") biocLite("hs133phsentrezgcdf") as was possible in past versions but package hs133phsentrezgcdf is not available in this version, I think. Your help is much appreciated! Apologies for this question! Min-Han

Hi Min-Han: > I have downloaded the CDF hs133phsentrezgcdf version 10, tar xvf done, > and moved the directory to > /home/minhan/R/x86_64-unknown-linux-gnu-library/2.9 > > Is that enough? I thought you need 'makecdfenv' to create a package (or an environment) from the CDF file. http://www.bioconductor.org/packages/release/bioc/html/makecdfenv.html ---- This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. ---- But then I am not sure in this particular case. Saroj > However, I get this error. > >> library(hs133phsentrezgcdf) >> > Error in library(hs133phsentrezgcdf) : > 'hs133phsentrezgcdf' is not a valid installed package > > Ideally, I would like to do > source("http://bioconductor.org/biocLite.R") > biocLite("hs133phsentrezgcdf") as was possible in past versions > but package hs133phsentrezgcdf is not available in this version, I think. > > Your help is much appreciated! Apologies for this question! > > Min-Han > > _______________________________________________ > 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 > >