[Bioperl-microarray] question about bioperl and microarrays

[Gavin Sherlock]

Hi Pavlos,

I don't believe that BioPerl has any facility for retrieving data  
from SMD, and SMD currently doesn't support querying of datasets to  
see if there exist data for a particular gene.  We have implemented a  
very basic set of Web Services (documented at http://genome- 
www5.stanford.edu/help/webServices.shtml), which we will flesh out in  
the future, but the easiest way to retrieve data currently from SMD  
is from our ftp site, which has data dumps for all published  
experiments organized by organism (ftp://smd-ftp.stanford.edu/pub/smd/ 
organisms/).  You would then have to parse the datafiles to determine  
if they had data for your gene(s) of interest,

Cheers,
Gavin
________________________________________________________

Gavin Sherlock
Dept. of Genetics
Center for Clinical Sciences Research
269 Campus Drive,
Room 2255b,
Stanford,
CA 94305-5120

Tel: 650 498 6012
Fax: 650 724 3701

On Oct 16, 2005, at 8:04 AM, pavlidis at imbb.forth.gr wrote:

> Hi,
> I would like to ask if there is any way using bioperl
> to retrieve microarray datasets from GEO or Stanford Database. I am  
> a newbie
> in bioperl and perl so I torture myself for days.
> Specifically I would like to retrieve all the datasets which have a  
> particular
> gene in them. Thank you very much
>
> Pavlos
>
> _______________________________________________
> bioperl-microarray mailing list
> bioperl-microarray at bioperl.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-microarray
>