[BioC] running exonmap package and chimp arrays

Michal Okoniewski michal at fgcz.ethz.ch
Mon Mar 9 09:25:46 CET 2009

Hi Pete,

Technically, a lot of functionality of exonmap is for annotation 
processing. It means in practice that if you want to translate
genes to exons and to probesets etc, you need a connection to X:MAP 
database that runs on MySQL .
The >8G RAM requirement is related mainly to the summarization (RMA) of 
exon array AffyBatch objects.

So the way around for your question 1) would be - to run summarization 
once elsewhere (where more RAM is available) and save the eSet object to 
a file, load it to your 2G computer connected to X:MAP and run all the 
exonmap pipelines for analysis. Just in
case you may want to save pairwise comparison outcome objects too.
Alternatively, you may summarize the data with xps package (it uses 
root.cern.ch schema to store the data outside the RAM), then use exonmap 
to analyze and visualize.

As for 2) - I have not heard about dedicated chimp array, however there 
were attempts to run chimp RNA on human exon array
(Affy chip has versions for Human, Mouse, Rat). Eg. a human tissue 
dataset was to be downloaded from Affy site.


Pete Shepard wrote:
> Dear Bioconductor list,
> I am brand new to Bioconductor and am interested in looking at exon arrays.
> I have two questions:
> 1) In the "common workflows" section of the getting started section, it says
> that to use the exonmap package I need >=8GB of RAM, I have 2GB. Is there a
> way around this?
> 2) Also I would like to look at human exon arrays and chimp/primate exon
> arrays. I am wondering if Bioconductor has a list of exon sets and data that
> are available to users?
> Thanks
> 	[[alternative HTML version deleted]]
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