[BioC] How to add annotation information?

[Marc Carlson]

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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>