[BioC] xmapcore get intronic sequence

[Tim Yates]

There are a couple of options:

1) Some of your probesets don't hit exons
2) Some of your probesets hit the same exons

Not much can be done if it's the first case, but you can detect the second
by passing as.vector=F to the probeset.to.exon method, ie:

> probesetIds = c( '3081222', '3081223' )
> probeset.to.exon( probesetIds )
[1] "ENSE00001149618"

> probeset.to.exon( probesetIds, as.vector=F )
RangedData with 2 rows and 6 value columns across 1 space
        space                 ranges |         IN1       stable_id    strand
  <character>              <IRanges> | <character>     <character> <integer>
1           7 [155592680, 155596420] |     3081222 ENSE00001149618        -1
2           7 [155592680, 155596420] |     3081223 ENSE00001149618        -1

You can see the IN1 column is the probeset name that caused the result, and
the stable_id column shows that both probesets hit the same exon

Fingers crossed this gets to the bottom of it ;-)

Cheers,

Tim

On 28/07/2010 15:56, "Stephen Taylor" <stephen.taylor at imm.ox.ac.uk> wrote:

> Hi Tim,
> 
>> probeset.to.exon( probesetids, rm.unreliable=F )
> 
> Unfortunately this is still not the same size:
> 
>> length(probeset.to.exon( probesetids, rm.unreliable=F ))
> [1] 1274
>> length(probesetids)
> [1] 1771
> 
> Thanks,
> 
> Steve