[Bioperl-microarray] Extraction of gene expression levels from NCBI GEO...

[Daniel Newkirk]

Hello all,
     I am new to this list, so bear with me if my question gets asked a lot. 
Being newer to bioinformatics, there are still many things I'm only now 
becoming familiar with. What I am trying to accomplish is to establish a 
method of retrieving Microarray data from NCBI's GEO database, specifically 
in connection with a particular gene. Once that data has been pulled in, it 
needs to be formatted to create a chart/report of basic expression levels in 
various tissue types. Projects like this have been done by Novartis at 
http://expression.gnf.org, retrieving the data points associated with a 
particular gene and then assembling the values into a java created graph. 
While easy to read, the tissue expression values are what I desire most over 
the graph.
     The problem with the aforementioned database is that all data is based 
on results from the Affymetrix U95A chip (human) and U74A chip (mouse) 
chips, which do not have probes corresponding to the most recent genes and 
ESTs. NCBI has data from the more recent U133A and B chips, as well as other 
array formats, and therefore is more likely to have the data I'm looking at, 
albeit the data being often derived from non-"normal" tissue. Initially, I 
expect to have to download the individual files from NCBI manually, and from 
that point parse the files with perl script and retrieve the expression 
values for the gene of interest. From that point, I can assemble a report 
combining the overlapping data points to create a proposed average 
expression level of Gene X in Tissue Y. The end of the matter is this: what 
modules are most suited to my purposes in Bioperl (if any) ? I have been 
browsing the docs and have not seen any that seem to apply to what I am 
doing, but I can easily miss something as there are so many modules in the 
latest release. Any ideas or suggestions would be most appreciated. 
Thanks!!!!!

Daniel Newkirk

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