[BioC] Affy normalization with custom chip.

[Cei Abreu-Goodger]

In this case, you're in luck. You can find both a .CDF file and a .probe
file for this chip:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1073

Cheers,

Cei

On Mon, 4 Jun 2007, Jenny Drnevich wrote:

> Hi Daniel,
>
> Also, there's a good chance that you won't be able to use gcrma() on
> a custom Affy chip, unless the custom array contains the PM-MM
> pairing, and you have a probe file that contains the amount and
> location of GC content of the probes, in addition to the cdf file. If
> it's a PM only array, you won't be able to do the gc-based background
> correction of gcrma, but you can do the model-based background of rma().
>
> Cheers,
> Jenny
>
> At 01:50 PM 6/4/2007, Cei Abreu-Goodger wrote:
>
> >Hi Daniel,
> >
> >I asked the same a while back. You should start by checking out
> >the "makecdfenv" and "matchprobes" vignettes. There should be enough
> >information there to get you going. Essentially you have to create your
> >own packages for the GNF1M chip and install them.
> >
> >Cei
> >
> >
> >On Mon, 4 Jun 2007, Daniel Gatti wrote:
> >
> > > I'm analyzing a publicly available GEO data set (GEO5961) that uses a
> > > custom array (GNF1M).  The file download from GEO includes a .CDF file
> > > for the array, CEL files and several other files that I'm not
> > familiar with.
> > >
> > >  > library(gcrma)
> > > Loading required package: Biobase
> > > Loading required package: tools
> > >
> > > Welcome to Bioconductor
> > >
> > >      Vignettes contain introductory material. To view, type
> > >      'openVignette()' or start with 'help(Biobase)'. For details
> > >      on reading vignettes, see the openVignette help page.
> > >
> > > Loading required package: affy
> > > Loading required package: affyio
> > > Loading required package: matchprobes
> > > Loading required package: splines
> > >  > rawdata = ReadAffy("GSM138562.CEL", "GSM138563.CEL")
> > >  > norm = gcrma(rawdata)
> > > Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> > > encountered:
> > > Specified environment does not contain gnGNF1Musa
> > > Library - package gngnf1musacdf not installed
> > > Data for package affy did not contain gngnf1musacdf
> > > Bioconductor - gngnf1musacdf not available
> > >
> > > How can I load the GPL1073.CDF and GPL1073.probe files for the array
> > > into the "environment" so that gcrma() can access them?  I've tried
> > > functions like getCDF(), but it's not clear how to specify a local file
> > > as the source.  And read.cdffile() reads into an object, but I'm not
> > > clear how make that object visible to gcrma().
> > >
> > > Thanks,
> > > Dan Gatti
> > > UNC-CH
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> >
> >
> >--
> >The Wellcome Trust Sanger Institute is operated by Genome Research
> >Limited, a charity registered in England with number 1021457 and a
> >company registered in England with number 2742969, whose registered
> >office is 215 Euston Road, London, NW1 2BE.
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >Search the archives:
> >http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
>


-- 
The Wellcome Trust Sanger Institute is operated by Genome Research 
Limited, a charity registered in England with number 1021457 and a 
company registered in England with number 2742969, whose registered 
office is 215 Euston Road, London, NW1 2BE.