Hi! I am trying to use bioconductor to analyze some affymetrix CEL files. However, I have run into some problems. Please excuse me if these problems have been explained before, but I couldn't find a solution on google or on the bioconductor and R web sites. I have two CEL files and one CDF file. The name of the cdf file is L_monocyto530090.cdf. I am using makecdfenv to make a package out of it. I have found out that the CDF file name seems to be specified in the CEL files, and in these files it is stated as L_monocyto530090.1sq. I have seen that bioconductor strips all non-letter/number characters from package names, so therefore I use this command to get the package name correct: make.cdf.package("L_monocyto530090.cdf", packagename="L_monocyto530090",package.path = "/med/adenine/u2/projects/listeria/packages") However, I encounter this error when I subsequently try to install it: adenine[14:41]:/med/adenine/u2/projects/listeria> R CMD INSTALL -l ./lib ./packages/L_monocyto530090 * Installing *source* package 'L_monocyto530090' ... Error: Invalid DESCRIPTION file Malformed package name See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed adenine[14:41]:/med/adenine/u2/projects/listeria> I understand that this is due to the underline character in the package name. I have also tried to manually change the name in the CEL files, but that only resulted in me corrupting the files. Is there any way I can work around this somehow? Thanks, Karin -- Karin Lagesen, PhD student karin.lagesen at medisin.uio.no http://www.cmbn.no/rognes/

Karin Lagesen wrote: > Hi! > > I am trying to use bioconductor to analyze some affymetrix CEL > files. However, I have run into some problems. Please excuse me if > these problems have been explained before, but I couldn't find a > solution on google or on the bioconductor and R web sites. > > I have two CEL files and one CDF file. The name of the cdf file is > L_monocyto530090.cdf. I am using makecdfenv to make a package out of > it. I have found out that the CDF file name seems to be specified in > the CEL files, and in these files it is stated as > L_monocyto530090.1sq. I have seen that bioconductor strips all > non-letter/number characters from package names, so therefore I use > this command to get the package name correct: > > make.cdf.package("L_monocyto530090.cdf", packagename="L_monocyto530090",package.path = "/med/adenine/u2/projects/listeria/packages") The problem here is that you are using the incorrect package name. Remove the packagename="L_monocyto530090" from your call to make.cdf.package(), and everything should work out fine. Note that affy will expect your cdfenv to be called lmonocyto530090cdf as well (which is what make.cdf.package() will call it). HTH, Jim > > However, I encounter this error when I subsequently try to install it: > > > adenine[14:41]:/med/adenine/u2/projects/listeria> R CMD INSTALL -l ./lib ./packages/L_monocyto530090 > * Installing *source* package 'L_monocyto530090' ... > Error: Invalid DESCRIPTION file > > Malformed package name > > See the information on DESCRIPTION files in section 'Creating R > packages' of the 'Writing R Extensions' manual. > Execution halted > ERROR: installing package DESCRIPTION failed > adenine[14:41]:/med/adenine/u2/projects/listeria> > > > I understand that this is due to the underline character in the > package name. I have also tried to manually change the name in the CEL > files, but that only resulted in me corrupting the files. > > Is there any way I can work around this somehow? > > Thanks, > > Karin -- 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