[BioC] how to map Affymetrix ID to ensemble gene ID

David Westergaard david at harsk.dk
Mon Mar 19 00:03:13 CET 2012

Dear Shan Gao,

Perhaps you can try this:

>ensembl <- useMart("ensembl", data = "sscrofa_gene_ensembl")
>filters <- listFilters(ensembl)

Looking through filters for anything related to affymetrix yields this:
> filters[grep("Affy",filters$description),]
                  name                                          description
9  with_affy_porcine                     with Affy Porcine probeset ID(s)
62      affy_porcine Affy Porcine probeset ID(s) [e.g. Ssc.25128.1.S1_at]

Now, try to read up on the example just before section 4 in the
biomaRt vigenette.

David Westergaard

2012/3/18 wang peter <wng.peter at gmail.com>:
> dear Nicolas Delhomme:
>        thx for your teaching. i donot want to argue with you. but
> if i do, i would u like to argue with a person i respect a lot.
>        so i do a little argue with u. first i am not peter, please see
> my name is shan gao.  second, my quesiton is very clear and
> concise. third, my case is special, it is pig genome. i donot think
> i can use getBM() function using "filters" and "attributes" (look at
> the listAttributes and listFilters function) to finish my work. how
> can you
> and other people think i am not familiar with the Biomart package.
> i can use it very well, but it cannot solve my problem.
>        and if all the people must read and solve the problem by themselves.
> why did they build this forum and mailling list?
>        if somebody did the same work and others will do, that is really
> WASTE of time.
> thank  you
> shan gao
> _______________________________________________
> 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

More information about the Bioconductor mailing list