[BioC] exonmap install

[Dick Beyer]

Hi Jim and Michal,

I made the mistake of using the xmap_mus_musculus_core_41_36b mysql files with the Ensembl  mus_musculus_core_43_36d mysql data.  The exonmap and Jim's exonModel routines work great when I used both xmap_mus_musculus_core_41_36b files and mus_musculus_core_41_36b data.

Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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 			Seattle, WA 98105-6099
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http://staff.washington.edu/~dbeyer
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On Mon, 26 Mar 2007, James W. MacDonald wrote:

> 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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