Hi all,

Not sure how I managed not to cc: the list on this initially. Here's some GO.db code with a sort of "moral" to it ;-)

--t

Begin forwarded message:

library(IlluminaHumanMethylation450k.db)

## allow both singly- and multiply-mapped probes (e.g. for SYMBOL) IlluminaHumanMethylation450kGOall <-toggleProbes(IlluminaHumanMethylation450kGO, 'all')

## now let's look at the differences that result from toggleProbes()
mapped_probes_default <- mappedkeys(IlluminaHumanMethylation450kGO)
mapped_probes_toggled <- mappedkeys(IlluminaHumanMethylation450kGOall)
multimapped <- setdiff( mapped_probes_toggled, mapped_probes_default )

res0 <- mget(head(multimapped), IlluminaHumanMethylation450kGO, ifnotfound=NA)
res <- mget(head(multimapped), IlluminaHumanMethylation450kGOall, ifnotfound=NA)

## fetch the GOIDs from the unencumbered toggled map, to get terms for them

library(GO.db)
GOids <- lapply(res, function(x) unlist(lapply(x, function(y) y$GOID)))
GOterms <- lapply(GOids, function(x) mget(x, GOTERM, ifnotfound=NA))
head(GOterms)


> I'll add this to the docs (next release)
> 
> thanks,
> 
> --t
> 
> 
> 
> On Fri, Mar 29, 2013 at 11:24 AM, Fabrice Tourre <fabrice.ciup@gmail.com> wrote:
>> Tim,
>> 
>> Thank you very much for your reply.
>> I have a list of probe list.
>> Do you a example script for me to get the GO terms, instead of GO ID?
>> 
>> The Documentation is not very clear for this.
>> http://www.bioconductor.org/packages/2.11/data/annotation/html/IlluminaHumanMethylation450k.db.html
>> 
>> On Fri, Mar 29, 2013 at 12:29 PM, Tim Triche, Jr. <tim.triche@gmail.com> wrote:
>> > Oddly enough, the paper from UCSD with Illumina's folks on it (*) used the
>> > IlluminaHumanMethylation450k.db package (which I am currently rebuilding to
>> > have a startup message about toggleProbes()) to annotate both CpG islands
>> > and GO terms.
>> >
>> > (*)
>> > http://idekerlab.ucsd.edu/publications/Documents/Hannum_MolCell_2012.pdf
>> >
>> >
>> > On Fri, Mar 29, 2013 at 8:49 AM, Fabrice Tourre <fabrice.ciup@gmail.com>
>> > wrote:
>> >>
>> >> Dear list,
>> >>
>> >> In the annotation file of Infinium HumanMethylation450 BeadChip,
>> >>
>> >> http://support.illumina.com/documents/MyIllumina/b78d361a-def5-4adb-ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv
>> >>
>> >> for each probe set, they do not have annotation for GO terms, pathways.
>> >>
>> >> As they have done in the annotation file: HG-U133_Plus_2.na32.annot.csv.
>> >>
>> >> Is there some bioconductor package to annotated the Infinium
>> >> HumanMethylation450 probes? Given a probe, feed back the GO terms and
>> >> pathways.
>> >>
>> >> Thank you very much in advance.
>> >>
>> >> _______________________________________________
>> >> 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
>> >
>> >
>> >
>> >
>> > --
>> > A model is a lie that helps you see the truth.
>> >
>> > Howard Skipper
> 
> 
> 
> -- 
> A model is a lie that helps you see the truth.
> 
> Howard Skipper

	[[alternative HTML version deleted]]

