[BioC] Using ReadAffy with custom CDFs on tiling array data

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Jul 28 16:16:42 CEST 2008

Hi Naira,

On Jul 28, 2008, at 9:57 AM, Naira Naouar wrote:

> Personally, I have been working on Arabidopsis Thaliana 1.0R tiling  
> array and I have produced my own CDF for this array. The way I did  
> it is explained here: http://wiki.fhcrc.org/bioc/DetailedScheduleTentative?action=AttachFile&do=get&target=Lightning-Naouar.pdf

Thanks for the slides! I've actually done something very similar for  
the Drosophila 1.0R tiling array in terms of realigning probes and  
annotating as exon/ambiguous-exon (ie, an exon in only 1 isoform of a  
transcript)/intron/intergenic/etc. The only question I have is what  
did you then use to get it back into the expected CDF format for  
seamless use in Bioconductor?

Sorry if I'm missing something, but I haven't come across a way to  
create a custom cdf w/o affy's bpmap and cif files ... did you create  
your own bpmap from your annotations (or something)?


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


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