[BioC] How to obtain a CDF file

[Mark Robinson]

Hi Aguera.

I'm not sure an AffyBatch object is the desired route for Affy tiling  
arrays.

One suggestion would be the combination of 'pdInfoBuilder' to build a  
package and oligo::read.celfiles() to read in your data.  See  
vignettes at:

http://www.bioconductor.org/packages/release/bioc/html/pdInfoBuilder.html

If you really really want a CDF file, you might check out:

http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-bpmap-files-tiling-arrays

... but there are a few judgement calls (e.g. splitting into  
"probesets" and so on) that I made there that may not be correct for  
what you need.

Hope that helps.
Mark


On 24/04/2009, at 6:35 PM, Elsa Aguera wrote:

> Hi every body,
> We have to analyse data from Affymetrix microarrays with  
> bioconductor and it's the first time we use bioconductor. We work  
> with drosophila melanogaster, the chip Type is Dm_tiling2_MR_v01. We  
> have a lot of .bpmap file (download in the site of Affymetrix) but  
> no cdf file. We can't work without cdf file, and we don't know how  
> to get a cdf file. When we try the function ReadAffy this message  
> appear :
>
> > ReadAffy("gfpc4.CEL")
> AffyBatch object
> size of arrays=2560x2560 features (7 kb)
> cdf=Dm_tiling2_MR_v01 (??? affyids)
> number of samples=1
> Error in getCdfInfo(object) :
> Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Dm_tiling2_MR_v01
> Library - package dmtiling2mrv01cdf not installed
> Data for package affy did not contain dmtiling2mrv01cdf
> Bioconductor - dmtiling2mrv01cdf not available
> In addition: Warning message:
> missing cdf environment! in show(AffyBatch)
>
> Actually my question is how we can do to get the cdf file call  
> dmtiling2mrv01.cdf  ?
> Or can we make a .cdf file with a .bpmap file ?
>
> Someone can explain and help us ?
> thanks
> Aguera
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852