[BioC] How to obtain a CDF file

[Steve Lianoglou]

Hi Aguera,

Regarding dealing with tiling arrays (sorry for top posting):

In addition to Marks' suggestions, you might want to have a look at  
the new AffyTiling package in Bioconductor 2.4, to see what they're  
doing (I haven't), as well as the older tilingArray and davidTiling  
packges :

* http://www.bioconductor.org/packages/release/bioc/html/AffyTiling.html
* http://www.bioconductor.org/packages/release/bioc/html/tilingArray.html
* http://www.bioconductor.org/packages/release/data/experiment/html/davidTiling.html

Lastly, look at MAT (and the new R-native Bioc 2.4 rMAT packages).  
They perform analysis over tiling arrays using the *.bpmap files only  
(I believe):

* http://liulab.dfci.harvard.edu/MAT/
* http://www.bioconductor.org/packages/release/bioc/html/rMAT.html

HTH,
-steve

On Apr 24, 2009, at 5:17 AM, Mark Robinson wrote:

> 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
>
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--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos