[BioC] affymetrix CDF file problem

[James W. MacDonald]

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