[BioC] exonmap install

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 23 19:15:39 CET 2007

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.



> 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
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> http://staff.washington.edu/~dbeyer
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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