[BioC] GO terms: Annotation for HumanMethylation450

[Marc Carlson]

Hi Fabrice,

Suppose you are using Tims package.

library("IlluminaHumanMethylation450k.db")

That would give you access to this object: IlluminaHumanMethylation450kGO

Which would allow you to get the GO IDs for all your probes etc.

So then I think your question is: how could you get the GO terms and the 
pathways?

Well how about doing this?

library(GO.db)
ids = c( "GO:0008150", "GO:0001869")  ## just for example..
result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))

That value in result could then be merged (using the merge method) to 
your previous results (the ones that have the GOIDs)


   Marc


On 03/29/2013 08:49 AM, Fabrice Tourre 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.
>
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