[BioC] Retrieve new informations for the probes used in th microarray!

[Sean Davis]

On Thursday 04 January 2007 09:34, Romain Desprat wrote:
> Dear bioconductor List,
>
> I have a file  with the name of my probes, the start and end position,
> sequence... and I want to know if this  probes is in Exon, intron and to
> get genomic features automatically.The goal would be to get all these
> results in one table.For one probe I can do it myself on USCS, but I want
> to do it for the 300 000 probes of my tiling array (nimblegen).
> Is there any package that could help me or does anyone did solve this issue
> ?

This is pretty simple to do via the UCSC table browser.  In brief, make your 
probes into a custom track.  Then ask for the overlap of your probes with 
exons, etc., in the Table Browser.  For more detailed instructions, there is 
a link on the UCSC pages to contact them.  Just copy your email to them and 
they will likely give you step-by-step instructions on how to do what you are 
asking within a few hours; they are quite helpful in general.

An alternative is to use the Galaxy server here (which seems to be down at 
this moment):

http://g2.bx.psu.edu/

Hope this helps.

Sean