[BioC] exonmap install

[James W. MacDonald]

Hi Michal,

Michal Okoniewski wrote:
> Dick, Jim, 
> 
> As for installing local Ensembl: some of the tables in Ensembl
> installations are not
> needed in exonmap but we cannot guarantee, that they will not be used in
> future 
> versions. And 16G of data fits with no problem to a normal hard disc
> capacity, so it 
> seems easier to download it as a whole, than to choose appropriate
> tables.

This just includes the e.g., mus_musculus_core_41_36b files, correct? In 
other words, if one downloads all the files in that directory and 
installs that should be sufficient.

Best,

Jim


> 
> 
> The idea of exonmap was mainly to process
> gene-transcript-exon-probeset-genome 
> annotations, but in includes bits of analysis, too. 
> Recently, from the version 0.1.7 in addition to the pairwise comparison,
> there are 
> functions for high-throughput alternative splicing searches, 
> according to what's in Affy white papers: splicing.index()
> and splanova() for MIDAS-like splicing ANOVA in the case of multiple
> treatments. There was also added the most fancy, heatmap-like plot for
> multiexonic 
> genes so far: gene.strip()
> 
> Cheers, 
> Michal 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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