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  [[alternative HTML version deleted]]