[BioC] exonmap install

[shirley zhang]

Hi Jim,

I am also working on Affy human all exon array data, could you also
send your functions to me?

Best,
Shirley

On 3/23/07, James W. MacDonald <jmacdon at med.umich.edu> 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
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>
>
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