[BioC] CDF file package for the Drosophila Affy chip

[Laurent Gautier]

On Mon, Dec 09, 2002 at 04:19:56PM -0500, Terry Gaasterland wrote:
> 
> Hello,
> 
> The Drosophila chip CDF file package is missing from the CDF
> data page at:
> 
>   http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> 
> All of the other chips that we are using are there.  Is the
> package for this chip in a special place?
> 

nop. everything we have in the shop is there I think.

> Do you need a copy of the original Affy CDF file for this chip?

yep. So we can add it to the collection.

> 
> Finally, since I have the CDF file but not a prepared package,
> is there a way for me to use the newest version of the R affy
> library with the CDF file directly?

You can do that too.

Here we go:

a) one way (*should* work... non tested):

library(affy)
 ## read your CEL data in 'myAffyBatch'

myname <- myAffyBatch@cdfName
 ## end R session
 ## have the CDF file named like <myname>.CDF
 ## and move it (or make a link) to your working directory with R
 ## start R again. You should not have to worry about the cdf environment

b) a another way:
 
library(affy)
 ## read your CEL data in 'myAffyBatch'

mycdf <- read.cdffile("path/to/my/file.CDF")
mylocationsenv <- getLocationsData.Cdf(mycdf, want.na=FALSE)

env.name <- myAffyBatch@cdfName
assign(env.name, mylocationsenv)

 ## then you can proceed without worrying about the cdf stuff...



Hopin' it helps,





L.


> 
> We are having lots of fun with the bioconductor tools!
> 
> Thanks!
> 
>   -- Terry
> 
> 
>     *****************************************
>     *****************************************
>                 TERRY GAASTERLAND
>            Associate Professor and Head
>       Laboratory of Computational Genomics
>            The Rockefeller University
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> 
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Laurent Gautier			CBS, Building 208, DTU
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