CHR does what is expected of the mapping in that it returns the chromosome
of the probe.   It is constructed by overwriting the bimap for CHR with
that for CHR37 on export.  Without this kludge, tens of thousands of probes
return NA as their chromosome, which is clearly incorrect.

As it happens, due to a long-standing tradition of excluding 'promiscuous'
probes, the default behavior of ALIAS2PROBE (for example) is also wrong.
 I'm about to upload 2.0.6 with that patched.

The problem with gene-centric annotations of the sort used in Bioconductor
.db packages is that they're gene-centric; the mapping from probes to
genes, locations, chromosomes, GO annotations, KEGG pathways, and the like
is done through EntrezGene IDs. There has been some discussion as to
whether completely reannotating the chip might not be a better idea in this
respect, i.e. mapping the probes to the nearest TSS.  As I have gained more
experience with the GRanges architecture, I have realized that GRanges are
the more sensible approach to annotating the probes on the 450k.

Nonetheless, the 450k.db package is out there so it ought to do what it's
expected to, unless or until everything transitions to the manifest package
that Kasper and Martin Aryee put together.


On Sun, Nov 6, 2011 at 11:00 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> In the package IlluminaHumanMethylation450k.db, there are three data
> objects relating probes to chromosomes. They are
> IlluminaHumanMethylation450kCHR, IlluminaHumanMethylation450kCHR36, and
> IlluminaHumanMethylation450kCHR37. I wonder what the reason of having
> IlluminaHumanMethylation450kCHR is, and what reference was used, since that
> is not explained in the help page of IlluminaHumanMethylation450kCHR ? Is
> it redundant ?
>
> Also, the mapping to locations, IlluminaHumanMethylation450kCHRLOC, is
> only available for hg19. There should also be one for hg18, or otherwise
> the IlluminaHumanMethylation450kCHR36 should not be supported.
>
> I am referring to version 1.4.6 of the IlluminaHumanMethylation450k.db
> package.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is. John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

	[[alternative HTML version deleted]]

