You will need to use toggleProbes() to get all probe locations (this is an
undesirable side effect of the db0 package infrastructure, which is geared
towards expression arrays where probes that map to multiple accessions are
a "bad thing", and that is the reason I deprecated the 27k.db and 450k.db
packages).

The FDb.InfiniumMethylation packages have the locations of the targeted
CpGs (and CpHs, and SNPs) for the corresponding build (just for the record,
the genome build targeted by 450k.db is hg19/GRch37), but they are returned
using get450k() or get27k() as a GRanges object.  In the near future I am
going to suggest that people migrate to minfi for processing, as the
terminal data structure emitted by recent versions of 'minfi' is also based
around a GRanges representation for the probes (it is a subclass of
SummarizedExperiment, which I have also been working on scaling up to
handle thousands of samples at a time).

Essentially, the mistake I made in compiling the 27k.db and 450k.db
packages was to use an expression-centric (or gene- and transcript-centric)
infrastructure to represent probes targeting individual loci.  It's more
useful to think of the 450k array, in particular, as a SNP array, with
functions for a given target locus inferred after discovery.  It's also
more useful to think of the chip as a SNP array when considering
differentially methylated regions, which could be loosely regarded as the
methylation equivalent of copy number variations.  Last but not least, you
can in fact use the array to estimate copy number along the genome, as for
determining sex from chrX copy number.



On Mon, Jul 1, 2013 at 10:35 AM, Simone <enomis.bioc@gmail.com> wrote:

> Hello!
>
> A little question: I've got a table with beta values obtained by
> Illumina's 450K BeadChip microarray and want to know for each probe
> where in the gene it is located (mainly promoter region or gene body).
> I found the IlluminaHumanMethylation450kPROBELOCATION function in the
> IlluminaHumanMethylation450k.db package which seems to do what I want,
> but not for all the probes.
> In detail, I have got data for 473,029 probes, but the function only
> returns values for 354,770 unique probes, so 118,259 ones are missing.
> Is this expected behaviour? Should I use another package to get
> location information for all the probes contained in my file?
>
> And secondly: As the IlluminaHumanMethylation450k.db package seems to
> be deprecated, on which build of the genome is the
> IlluminaHumanMethylation450kPROBELOCATION information based? Because I
> see that in the package there are some separate functions for build 36
> respectively 37, but in the help of the function in question I can
> only find the information that mappings are based on data of Illumina
> from January 2011 (which should then be GRCh37, the build I have to
> work with in this case, but however I am not completely sure as it
> doesn't say it clearly).
>
> Best regards,
> Simone
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
> LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
> LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
>  [1] sqldf_0.4-6.4                         RSQLite.extfuns_0.0.1
>  [3] chron_2.3-43                          gsubfn_0.6-5
>  [5] proto_0.3-10                          RColorBrewer_1.0-5
>  [7] illuminaHumanv2.db_1.18.0
> IlluminaHumanMethylation450k.db_2.0.7
>  [9] IlluminaHumanMethylation27k.db_1.4.7  org.Hs.eg.db_2.9.0
> [11] RSQLite_0.11.4                        DBI_0.2-7
> [13] AnnotationDbi_1.22.6                  affy_1.38.1
> [15] Biobase_2.20.0                        BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.28.0         AnnotationForge_1.2.1 BiocInstaller_1.10.2
> IRanges_1.18.1
> [5] preprocessCore_1.22.0 stats4_3.0.1          tcltk_3.0.1
> tools_3.0.1
> [9] zlibbioc_1.6.0
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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