Hi Min-Han -- Min-Han Tan <minhan.tan at="" gmail.com=""> writes: > 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 Use something like R CMD INSTALL --clean hs133phsentrezgcdf.tar.gz to install packages from the command line. I'm not really sure why this cdf is not available via biocLite, but will try to find out. Martin > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793