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

Nicolas Delhomme delhomme at embl.de
Sun Mar 18 23:18:08 CET 2012

Dear Peter,

I think you misunderstood Hervé's answer. The point was not about doing your research in 10 minutes, but if you know someone that can do my research in ten minutes, I'd glad to hire him/her :-).

 The points were :

1) by looking in the documentation you'll learn more about these packages. It will always be helpful for you even if it does not give you the answer. It will give you a better understanding of the package functionality and help you describe your problem better. This is essential, you'll see next.

2) Sean already gave you an answer to that question, namely to look at the getBM() function. From your answer to his email, it seemed (note that I don't know what you did) that you had not investigated the matter much further. I say it "seemed" because you formulated your email almost exactly in the same way as your original one, demonstrating no progress in your thoughts about the problem. Again here I don't know what the truth is, I'm just saying how it came out.

Now it is important to understand that the exchange on this list and especially the answers are given freely by people on their own time (I spend my 10+ mins answering you) so that it benefits all of us as a whole. I hope that you understand it is essential for the people asking questions to be concise, precise and respectful of the work of others. By showing progress in your problem consideration and suggesting new approaches, you would then elicit another answer and by this step-wise process you'll likely end up with a solution to your problem. It will cost you time, and to the people answering you too, but it is no lost time, because you'll get a solution in less time that it would have taken you to get it alone, plus it might benefit other list members. That is the spirit of this list and it needs to remain so, otherwise less and less people will be willing to answer questions and all of us will be on our own to solve our problems.

Now to your problem; if the function you are looking for does not exists, you might have to write it on your own. The starting point is the getBM() function. You need first to connect to a mart database (look at the useMart, listMarts, listDataset functions) and then use the getBM() function using "filters" and "attributes" (look at the listAttributes and listFilters function) to retrieve the information about the affy probes you're interested in. Look at the biomaRt vignette for the details on that. Note that I was in the same situation as you three years ago and I made my way through the vignette to get to my solution. R and Bioconductor do have a lot of documentation and reading it is no loss of time, I hope I made that clear.

Finally, if the getAffyArrays function does not exist but is stated in the documentation, then you need to report that in your original email. The more you explain, the more likely you are to get a quick answer.



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 22:27, wang peter wrote:

> dear Hervé Pagès:
>       thank you for your reply, but i donot think there are
> some people can find my answer in 10 mins. if you know
> who can, i will stop my research and feel ashamed and
> kill myself.
>       anyway, i read the examples which said there is a
> getAffyArrays() ,but there is no. it mislead me and killed
> more than 10 min of me
>        thank u. anyway, my case is special, it is pig microarray,
> not human, mouse
> -- 
> shan gao
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> Boyce Thompson Institute
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