[BioC] exonmap install

[Dick Beyer]

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_musculus_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
>> 
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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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