[BioC] affymetrix CDF file problem

Karin Lagesen karin.lagesen at medisin.uio.no
Thu Jun 16 15:51:20 CEST 2005


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

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? 


Karin Lagesen, PhD student
karin.lagesen at medisin.uio.no

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