[BioC] How to obtain a CDF file
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Fri Apr 24 16:33:13 CEST 2009
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
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
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:
> If you really really want a CDF file, you might check out:
> ... 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.
> 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 ?
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 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
> Bioconductor mailing list
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> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
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