Keith Ching wrote:
> Hi,
> 
> I am looking into using BASE2 to store ChIP-chip data from the NimbleGen 
> platform.
> Each whole genome scan has 14 million probes, divided up into 38 arrays 
> of 370k probes each.
> 
> What is the feasibility of storing this information in BASE2?  Say we 
> had 100+ whole genome scans.
> Would it even be practical?  Should I just store the raw datafiles as 
> file attachments?  It would be nice
> to have some compression built into the file attachments as this could 
> save 75% on the disk space as each
> expt is 3 gigs or so.

Wow, that is really a lot of data. I wouldn't store that in the 
database. It would suck the performance out of the entire application. 
You could compress the files before you upload them to Base 2. Or, you 
could let the operating system automatically compress the folder where 
the file uploads are stored.

Note however, if you store the data in files, you will not be able to 
use any of the existing plugins to analyze the data. If you want to do 
that you will need to create a plugin that generates a more managable 
data set from the files. We have created such a plugin for Affymetrix 
files. See http://lev.thep.lu.se/trac/baseplugins/wiki/thep.lu.se.RMAExpress
for more information about it.

/Nicklas


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