
Thanks for these information.

Regarding your proposal of using the remapped probe packages that are released through the 
Bioconductor project for which we do have windows packages:
1- Are those which are named CustomCDF ? 
2- The way to use these is not clear for me (if these are the one to be used) there are multiple files for a given chip and what they represent, how they have been built, and how to use these (for instance for affy chips using gcrma) is not clearly explained (unless I have missed something somewhere..?). Could it be possible to obtain a little bit of help on this from the BioC group.... 
Thanks again
Philippe Guardiola, MD


-----E-mail d'origine-----
De : Robert Gentleman <rgentlem@fhcrc.org>
A : phguardiol@aol.com
Cc : Bioconductor@stat.math.ethz.ch
Envoyé le : Je 8 Novembre 2007 8:27
Sujet : Re: [BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows



It looks like you are using windows and they do not provide packages for 
indows users. The reason they are not recognized by R is that they 
on't work.
Your options are to
) install enough tools on your computer to build packages (details can 
e found on CRAN)
) use the remapped probe packages that are released through the 
ioconductor project for which we do have windows packages
I have no idea what the intentions of AffyProbeMiner are, they have 
ever submitted anything, and until they do, it won't even be considered,
  best wishes
   Robert

hguardiol@aol.com wrote:
 Dear colleagues,
 
 
 I m trying to use the AffyProbeMiner packages available from 
ttp://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace 
he usual CDF probes and annotation files available in BioC.
 
 I m using R 2.6.0 under WinXPPro SP2.
 I have downloaded the files available on the webpage above in the R library 
older. 
 These are gz.rar compressed files and are not recognized in R windows : 
ackages -> Install packages from local zip files. 
 I have used WinRar to uncompress these files and have copy and paste 
he?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: 
gu133ageneccds_1.1.0) in the R folder library.??
 
 Then if I type:
 ?> library(hgu133ageneccds)
 
 I obtain the following error:
 Error in library(hgu133ageneccds) : 
 ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0?
 The same is true for all of these files
 
 Is it a problem of compatibility with R (too old files ?) ? Should I use a 
ifferent way to install these packages in R 2.6.0 ?
 
 
 Is there a plan to include these files and their update in BioC metadata ?
 
 
 Thanks for your help
 and hoping that this request will not be out of scope from this list since it 
s not a bioconductor package.
 
 Philippe Guardiola, MD
 
 
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obert Gentleman, PhD
rogram in Computational Biology
ivision of Public Health Sciences
red Hutchinson Cancer Research Center
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