[BioC] GO terms: Annotation for HumanMethylation450

[Jinyan Huang]

Marc Carlson,

Thank you. When I try your code, I have this problem.

> library(GO.db)
> ids = c( "GO:0008150", "GO:0001869")  ## just for example..
> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))
Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found

On Tue, Apr 2, 2013 at 5:03 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor



--
Best wishes,

Jinyan HUANG