Hiya!

It depends what sort of output format you want for your data.

For example, say you are interested in 'ENST00000413465' (a transcript of
TP53)

http://bit.ly/e9rSMg

You could do the following:

> probe.rd = xmap.range.apply( transcript.details( 'ENST00000413465' ),
function( ch, s, e, st ) probes.in.range( ch, s, e, st, as.vector=F ) )
> ranges( probe.rd ) = shift( ranges( probe.rd ), -start( transcript.details(
'ENST00000413465' ) ) )
> probe.rd

RangedData with 297 rows and 3 value columns across 1 space
          space         ranges   |                  sequence probe_hit_count
strand
    <character>      <IRanges>   |               <character>       <numeric>
<integer>
1            17     [215, 239]   | ATTAGCTGGGCATGGTGGCACGTGC               2
-1
2            17     [216, 240]   | AATTAGCTGGGCATGGTGGCACGTG               2
-1
3            17     [556, 580]   | CGTAAGCCAAGATCCAAAGAAAATG               1
-1
4            17     [597, 621]   | CAGAGCCTGTATGCAGAAGACCACA               1
-1
5            17     [758, 782]   | CCCAGGAGGCAGAGATTGCAGTGAG               2
-1
6            17     [762, 786]   | TGAACCCAGGAGGCAGAGATTGCAG               2
-1
7            17     [769, 793]   | AATCACTTGAACCCAGGAGGCAGAG               2
-1
8            17     [825, 849]   | CCAGCTATGGTAGTGTAAGCCTGTA               1
-1
9            17     [956, 980]   | GGGCATGGTGGCTCACACCTGTAAT               2
-1
...         ...            ... ...                       ...             ...
...
289          17 [23912, 23936]   | TGCCTACCAAGTCACAGACCCTTTT               1
-1
290          17 [24128, 24152]   | AGGAGGCGGAACTCGAATTCATTTC               1
-1
291          17 [24401, 24425]   | GCAAGCCCGGAGGTATTTTCAAGAA               1
-1
292          17 [24624, 24648]   | AGGCCGGTTCCTCTTACTTGGCAGA               1
-1
293          17 [24681, 24705]   | GGAGCAGCTCACTATTCACCCGATG               1
-1
294          17 [24871, 24895]   | CCGGCTCCGCTAGATGGAGAAAATC               1
-1
295          17 [24985, 25009]   | ACTGGGGCTCCATTCCGAAATGATC               1
-1
296          17 [25150, 25174]   | CTTGAGCCGGCCTAAAGCGTACTTC               1
-1
297          17 [25372, 25396]   | GGGCTCTCGGCTCCGTGTATTTTCA               1
-1

So, that is all 297 probes that hit inside the range of the transcript, with
the start and end of each probe relative to the start of the transcript

Tim


On 14/03/2011 18:17, "ekspiulo" <ekspiulo@gmail.com> wrote:

> 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.
> 
> e.g.
> 
> transcript-id: [ [probe-id, start, end], [probe-id, start, end], ... ]
> 
> 
> Thanks!
> 
> -Brian
> 
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