[Biopython] Retieving CEL Files from GEO

[Laurent]

>
> On Thu, Feb 17, 2011 at 3:59 PM, SHARANYA RAGHUNATH<
> sharanya.raghunath at utah.edu>  wrote:
>
>> Hello,
>>
>> I understand that there is a way to parse through the GEO data repository
>> in Biopython; however, is there a way to download the actual CEL files or
>> the SOFT files using a GSE or GDS id?
>>
>>
> Hi, Sharanya.
>
> You might take a look at both the GEOquery and GEOmetadb Bioconductor
> packages.  I know it is not a biopython solution, but I wanted to make sure
> that you were aware of them.  However, where the raw data are available (and
> they are not always available), you can simply download them from the NCBI
> ftp site:
>
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/
>
> Sean
>
> Disclaimer: I may be slightly biased about the relevance of the above
> software packages....
>

A similar question on this list received a similar answer (
http://lists.open-bio.org/pipermail/biopython-dev/2010-March/007503.html
), and despite the disclosed bias in the answer it was spot on (or so I 
heard). If you have a way to call R from Python, you can immediately use 
libraries available in R.

Disclaimer: The above answer tries to avoid biases regarding the 
relevance of a specific software package. ;-)