anyone with genomewide microarray analysis experience ?

[trias]

Hi,

I am trying to analyse some biological data from microarray experiments.
Different experiments have been stored in a SQL database.

One of the things I would like to do is to fetch all data from a certain
distance from gene ATGs say 100+/- bp and calculate the bp average over all
genes over this region.

The microarray data has been normalised over each bp

Does anyone have some scripts I could use for this purpose. I work with
S.cerevisiae

Thank you
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[Istvan Albert]

On Aug 14, 8:52 am, trias <t.gkikopou...@dundee.ac.uk> wrote:

> Does anyone have some scripts I could use for this purpose. I work with
> S.cerevisiae

Since the largest chromosome on the yeast genome is around 4 million
bp, the easiest way to accomplish your goal is to create a list of the
same size as the chromosome, then populate this list by mapping the
genomic index to the list index.

After doing this your problem simplifies to slicing the list around
the coordinates of interest.

You'll be done in minutes.

i.

[Jochen Schulz]

trias:

>
> One of the things I would like to do is to fetch all data from a certain
> distance from gene ATGs say 100+/- bp and calculate the bp average over all
> genes over this region.

I know absolutely nothing about your problem domain, but if your
distance function is metric, you can use this:

http://well-adjusted.de/mspace.py

or that:

http://code.activestate.com/recipes/572156/

The latter (by Baerophile) is fast, the former (by me) has more
features. Baerophile has even faster implementations (non-Python) as
well.

J.
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