[BioC] Problem with some exonmap X.to.Y functions

[Crispin Miller]

Hi Sophie,
Taking the last bit first - the bug in plot gene you have has been fixed
- please can you update exonmap to version 1.0.06.

---
As far as the other problems you were having, I'm a bit confused... What
version of the X:MAP database are you using - and what version of
Ensembl?

I've just checked things on our installation here:

Using exonmap (and corresponding Ensembl download) version:
homo_sapiens_core_45_36g

I get:

> probeset.to.exon("3102398")
[1] "ENSE00000697174"
> exon.to.probeset("ENSE00000697174")
[1] "3102398"
> probeset.to.transcript("3102398");
[1] "ENST00000260128"
> probeset.to.gene("3102398");
[1] "ENSG00000137573"


But...
According to X:MAP, '3102398' is a probeset targeting SULF1, not TP53:

http://xmap.picr.man.ac.uk/#8/70650974/15/h

Again, "ENSG00000137573" is SULF1 and ENST00000260128 and
ENSE00000697174 are both transcripts and exons within that genem and the
probeset->exon->transcript->gene hierarchy is what you would expect.

I won't post the full output of testing, but I get sensible answers back
for the rest of your queries too.

Crispin
 
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