[BioC] exonmap install

[Michal Okoniewski]

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.  


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 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer
Sent: 23 March 2007 20:02
To: James W. MacDonald
Cc: Bioconductor
Subject: Re: [BioC] exonmap install

Hi Jim,

Thanks for letting me know you were successful with just the
homo_sapiens_core_43_36d dataset.  I will try that with the mouse.

And I would love to take you up on your kind offer to try your new
functions. Using super-pre-alpha makes me feel alive :-)

Cheers,
Dick
************************************************************************
*******
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
************************************************************************
*******

On Fri, 23 Mar 2007, James W. MacDonald wrote:

> Hi Dick,
>
> Dick Beyer wrote:
>> Has anyone done the complete install of the mysql Ensembl databases 
>> that are used by the exonmap package?  The sizes of some of the 
>> database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting.
>> 
>> I am using the affy mouse exon arrays and wondered if, initially at 
>> least, I could just install some smaller portion of all the 
>> recommended data in order to do a gene core analysis?  That is, could

>> I just install, say, the files from:
>> 
>> ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_musculu
>> s_core_43_36d
>
> I have installed the xmap stuff for the human exon arrays, and all I 
> needed were the homo_sapiens_core_43_36d files. Does the INSTALL.TXT 
> that comes with the mouse version differ in what they say you need to 
> download? Naively I would assume what you need would be the same (only
mouse, not human).
>
> As an aside, I have some functions I wrote to do what I think is a 
> more reasonable analysis of these data than simply doing loads of 
> t-tests for each probeset. If you are interested I can send them to 
> you. I would be interested in any feedback you might have.
>
> Note that these are bare functions, not a package, and I just started 
> writing them this week so they are in super-pre-alpha status ;-D.
>
> Best,
>
> Jim
>
>
>> 
>> 
>> rather than of the files from current_mus_musculus?  And could I 
>> delay installing the "Multi-species data" and the "BioMart data"?  Or

>> do the commands I would use to get a core gene list from the exon CEL

>> files need to access all those database tables?
>> 
>> Thanks much, Dick
>>
************************************************************************
*******
>>  Richard P. Beyer, Ph.D.	University of Washington Tel.:(206) 616
7378
>> Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696	4225
>> Roosevelt Way NE, # 100 Seattle, WA 98105-6099 
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>> 
>> _______________________________________________ Bioconductor mailing 
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>
>
> --
> 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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