This is a result of CHR being derived from Entrez Gene mappings of
accessions, while CHR37 (from Illumina's manifest v1.1) is from the
hg19-aligned target sequence.

I think the right thing to do is to clobber the Entrez Gene-derived version
of CHR with the version from the Illumina manifest (CHR37) since, if a probe
is not annotated to an EG ID, org.Hs.egCHR returns NA, thus
IlluminaHumanMethylation450kCHR = NA.  The expected behavior would instead
be as implemented in CHR37.

So the expeditious way to resolve this appears to be clobbering CHR with
CHR37.

I'll upload version 1.4.7 with this fix (and several others, such as
exporting SNP and SNP10 maps) in the next few days.  I had hoped that there
was a more elegant solution to this and a couple of other issues related to
accession mappings, but it is more important for the package to behave as
expected than for it to be elegant.



On Tue, Jul 5, 2011 at 4:41 PM, David Martino <david.martino@mcri.edu.au>wrote:

> Dear list,
>
>
>
> We've noticed an apparent inconsistency in the bioc.db annotation file
> for the Illumina Human Methylation 450k arrays.
>
>
>
> IlluminaHumanMethylation450kCHR has some probes that aren't mapped to a
> chromosome but do have chromosomal locations
>
>
>
> Anyone using the 450K arrays will no doubt be running the development
> version of lumi in R-devel so I'm not sure if the .db annotation file
> has been updated but hasn't made it across to R-devel
>
>
>
> Eg
>
>
>
> x<- IlluminaHumanMethylation450kCHR
>
> # Get the probe identifiers that are mapped to a chromosome
>
> mapped_probes<- mappedkeys(x)
>
> # Convert to a list
>
> xx<- as.list(x[mapped_probes])
>
>
>
> summary("cg00000165" %in% names(xx))
>
>      Mode   FALSE    NA's
>
> logical       1       0
>
>
>
> but if I look at the files that come with 450 data, I can see
>
>  cg00000165 is mapped to chr 1
>
>
>
>
>
> Has anyone else encountered this?
>
>
>
> > sessionInfo()
>
>
> R version 2.14.0 Under development (unstable) (2011-07-02 r56248)
>
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
>
> locale:
>
>
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>
>
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>
>
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>
>
>  [7] LC_PAPER=C                 LC_NAME=C
>
>
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
>
> attached base packages:
>
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
>
> other attached packages:
>
>
> [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0
>
>
> [3] RSQLite_0.9-4                         DBI_0.2-5
>
>
>
> [5] AnnotationDbi_1.15.9                  lumi_2.5.1
>
>
>
> [7] nleqslv_1.8.5                         methylumi_1.9.0
>
>
>
> [9] Biobase_2.13.7
>
>
>
>
>
>
>
>
>
>
> David Martino
>
> Research Officer
>
> Cancer and Disease Epigenetics
>
> Murdoch Childrens Research Institute,
>
> Flemington Road Parkville VIC 3052
>
>
>
> p 61 3 8341 6205       f 61 3 9348 1391        www.mcri.edu.au
>
>
>
>
> ______________________________________________________________________
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>



-- 
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>

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