[BioC] Re : Question about reannotated Affy annotation files - Question about AffyProbeMiner in R260 under windows

[Jarno Tuimala]

Hi!

The methodology of generating these remapped probes packages is described 
in NAR, and on the the web. See:

http://nar.oxfordjournals.org/cgi/content/full/33/20/e175
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm

There is also an example of how to use these package at the end of 
the readme page.

In addition to Bioconductor, you can download the probe packages from:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v10.asp

If you check the list on this site, you'll see that there are several 
packages for the same chip. These packages are based on different genome 
features (gene or transcript) or on different databases (Unigene, RefSeq, 
Entrez Gene, Ensembl, Vega).

Note that in order to be able to use GCRMA, you need to install both CDF 
and probe packages for your chip.

Best wishes,
Jarno


On Thu, 8 Nov 2007 phguardiol at aol.com wrote:

>
> 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 at fhcrc.org>
> A : phguardiol at aol.com
> Cc : Bioconductor at 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 at 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
>
>
>   [[alternative HTML version deleted]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
> -- 
> obert Gentleman, PhD
> rogram in Computational Biology
> ivision of Public Health Sciences
> red Hutchinson Cancer Research Center
> 100 Fairview Ave. N, M2-B876
> O Box 19024
> eattle, Washington 98109-1024
> 06-667-7700
> gentlem at fhcrc.org
> _______________________________________________
> ioconductor mailing list
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> earch the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> 	[[alternative HTML version deleted]]
>
>

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Jarno Tuimala, FT, bioinformatiikan asiantuntija, CSC, PL 405, 02101 Espoo 
puh.: (09) 457 2226, fax: (09) 457 2302, s-posti: jarno.tuimala at csc.fi
CSC on tieteen tietotekniikan keskus, http://www.csc.fi/molbio

Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland 
tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala at csc.fi
CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio
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