Dear Bioconductor users,

I am trying to build a custom .cdf file for a custom
Affymetrix genechip for an atypical model. The genechip has many features:
orfs, SNPs, introns/exons (for one chromosome), antisense etc… I believe the
design is fairly unique (PMID= 20974003; http://www.biomedcentral.com/1471-2164/11/603/table/T1)
but as far as I understand the default .cdf file is only for the control affy
probesets and orfs.


I want to integrate the other features in my own .cdf file.


Alternatively, I know multiple .cdf exist (http://ancillary.toxodb.org/docs/Array-Tutorial.html
in Library files), as built by Affymetrix (I imagine?) for SNPs and introns and I was wondering if
there is a way to combine multiple cdf files into one for example.
I have easy access to all the probe sequences of the arrays and their description. I do not have a finalized annotation package for the organism yet.I though there would be a package to create a cdf file from scratch but if it exists I cannot find it. As far as
I understand makecdfenv does not do that. I looked in the archive and over the web but could not find any info.
Thanks in advance.
Olivier


 









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