[BioC] How to add annotation information?

[Peng Yu]

Hi Marc,

I am using Affymetrix Mouse Gene 1.0-ST Array. I should ask the person
who did the experiment which version the array is, right? Base on the
version, I should use either mogene10stprobeset.db or
mogene10sttranscriptcluster.db, right?

I have read the document, but I am still not sure what command I
should use to convert the id to the annotation. Suppose I should use
mogene10stprobeset.db, would you please let me know what commands I
should use?

Regards,
Peng

On Tue, Jul 28, 2009 at 9:56 AM, Marc Carlson<mcarlson at fhcrc.org> wrote:
> Hi Peng,
>
> What platform are you using?  You can probably find an annotation
> package here that will contain all three types of annotation requested.:
>
> http://www.bioconductor.org/packages/release/data/annotation/
>
> If not you can make a chip package that will meet you needs by following
> the instructions here:
>
> http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html
>
>
>
>  Marc
>
>
>
>
> Peng Yu wrote:
>> Hi,
>>
>> I use the following code to normalized the data. It seems that the
>> data file has the Affimetrix id. I would like to includes MGI gene
>> symbol, Entrez gene symbol, gene description in the output file. I am
>> wondering if there is a way to do so with BioC. What command I should
>> use?
>>
>> Regards,
>> Peng
>>
>> library(oligo)
>> data<-read.celfiles(list.celfiles())
>> eset<-rma(dat)
>> eset<-rma(data)
>> write.exprs(eset, file="output.txt", sep="\t")
>>
>> The data look like the following.
>>
>>         koA-mth_HZ_5238_MST1_19389.cel  koB-mth_HZ_5238_MST1_19390.cel
>>  koC-mth_HZ_5238_MST1_19391.cel  koD-mth_HZ_5238_MST1_19392.cel
>> wt1-mth_HZ_5238_MST1_19385.cel  wt2-mth_HZ_5238_MST1_19386.cel
>> wt3-mth_HZ_5238_MST1_19387.cel  wt4-mth_HZ_5238_MST1_19388.cel
>> 10344615        7.07210987006919        7.01089258722033
>> 7.26426270000726.92980486555595 7.72857978063884
>> 6.91124431275741        7.457761829613277.21025349865986
>> 10344617        3.02519545040591        3.08697023169755
>> 3.032032340858283.09846420636071        3.12487891156704
>> 3.10727683101607        3.0544609560487 3.03353963677405
>> 10344619        3.20294677833793        3.20612630466463
>> 3.176553031536723.13210443165341        3.1378507207366
>> 3.21452663497659        3.313450502242243.09287042099817
>>
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>
>