[BioC] xmapcore

ekspiulo ekspiulo at gmail.com
Mon Mar 14 19:17:57 CET 2011

Hello all,

I'm endeavouring to produce transcript relative coordinates for the 
probe sets on an affymetrix exon st array.  I've normalized the data at 
the probe set level using the oligo package, and I want to use the xmap 
projects annotations, but for the life of me I can not figure out how to 
query its data in a fashion that can produce either a single coordinate 
range or even the set of all possible coordinate ranges for a probe set, 
can anyone tell me where to start with this?

Alternatively, can I get probe level data from the normalized results 
from Oligo, and does it even make sense for an exon array?  I'm doing 
some custom alternative splicing analysis, so ideally I'd be able to get 
the data needed to produce a list of all of the probes/probesets which 
target each transcript in xmap along with either the genomic coordinates 
for those probes/probesets or their transcript relative coordinates.


transcript-id: [ [probe-id, start, end], [probe-id, start, end], ... ]



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