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

[Nicolas Delhomme]

Dear Shan Gao,

Sorry for the name mistake, but your email come as that of "wang peter".

Here is how I would you do:

mart <- useMart("ensembl")
listDatasets(mart)

## I suppose the 45th entry is what you want  (Pig = Sus scrofa)
listDatasets(mart)[45,]
mart <- useDataset("sscrofa_gene_ensembl",mart)

## Here we get lucky at position 53
grep("affy",listAttributes(mart)[,1])
listAttributes(mart)[53,]

## So now you can do your getBM query to get your affy probeset and related information
## (well extend the command obviously with what you need)
getBM("affy_porcine",mart)

Note:
1) I did not know that dataset before
2) I've never retrieved affy IDs before that way, but I knew it was possible through my previous readings of the documentation

3) I like to argue with you too, so
a) your question was actually too concise (the more details the better)
b) precise in your email that you are familiar with biomaRt (it would avoid such answers as before, and get you useful ones). Just tell me how we could know from your posts that it was otherwise?
c) post your code and where you're stuck
d) as I said it's a step by step process. You have an issue, you post it with details, you get an answer, you work until the next problem, etc.
e) Again as I said, it's my free time and free will to answer you. This list is made so that people do get help when they need, and it's a reciprocal process. Next time I have an issue, maybe you can help. And for that you would need as much info from me as possible, right?

Anyway, I hope this helps. If that solution still does not give you the information you need, then post again on the list explaining in details why not and what you are looking for.

Best,

Nico

> sessionInfo()
R version 2.14.1 Patched (2011-12-23 r57982)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.9-5  tools_2.14.1 XML_3.9-2


---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 18 Mar 2012, at 23:29, wang peter wrote:

> 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