[BioC] affy: CDF packages

[Laurent Gautier]

The function "getLocationData.Cdf" will help you to create
an environment from the CDF file (read using read.cdffile).
The section 'configure the options' of the vignette should
help to figure out how to use directly an environment to
get the mapping (get back to me if it does not).

Hopin' it helps,


L.



On Thu, Nov 21, 2002 at 08:58:41AM -0500, Sundaram, Shyam (NIH/CIT) wrote:
> Pawel:
> You can actually load your own CDF file. There are two approaches to this. 
> (1)  ReadAffy(CDFfile=NULL, CELfiles=NULL,widget=FALSE,
>               compress.cel=FALSE,compress.cdf=FALSE,
>               verbose=TRUE, chip.names=NULL,rm.mask=FALSE,
> rm.outliers=FALSE,
>               rm.extra=FALSE, cdf.name = NULL,  phenodata=NULL,
>               annotation="", description="", notes="", ...)
>   This will create the plob with the CDF object, CEL objects combined.
>  
> (2) read.cdffile(file, compress=TRUE)
>     This will allow you to read a cdf file alone and store as an cdf object.
>  
>  
> Hope this helps.
>  
> Shyam
> 
> -----Original Message-----
> From: Pawel Herzyk [mailto:ph53d@udcf.gla.ac.uk]
> Sent: Thursday, November 21, 2002 8:29 AM
> To: bioconductor
> Subject: [BioC] affy: CDF packages
> 
> 
> Dear CDF package maintainer,
>  
> It appeared to me that the web site for Affymetrix Data Packages does not
> contain two packages corresponding to CDF files for two important chips
> namely:
>  
> DrosGenome1.CDF - this is the current Drosophila chip
> ATH1-121501.CDF - this is a new Arabidopsis Chip released earlier this year.
>  
> Also:
> Is there any way that the user can use the actual CDF file or is he now
> entirely dependent on the appropriate package being timely placed in the
> bioconductor web-site?
>  
> regards
> Pawel
>  
> -----------------------
> Dr. Pawel Herzyk
> p.herzyk@bio.gla.ac.uk <mailto:p.herzyk@bio.gla.ac.uk> 
> Head of Bioinformatics
> 0141-3303180
> The Sir Henry Wellcome Functional Genomics Facility
> Institute of Biomedical and Life Sciences
> Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ
>  
>  
> 

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PhD. Student			DK-2800 Lyngby,Denmark	
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