[BioC] CDF package needed for Barley chip

[lshen]

Hello:

I made it for Windows, plus Linux. 

For windows version, you may get it at:

http://barleypop.vrac.iastate.edu/BarleyBase/testls/rpackage/barley1cd
f.zip

Installation need some other tools:

For windows, you need to get tools from:
http://www.stats.ox.ac.uk/pub/Rtools/tools.zip (sources), which is
under http://www.stats.ox.ac.uk/pub/Rtools/


1. Get the tools, and unzip it to the ...R\bin\ directory
2 .Unzip the barley1cdf.zip to a directory, i.e. c:\barley1cdf

3. Under command line cd to ..R\bin\ directory, run:
RCMD INSTALL --docs=normal c:\barley1cdf

This works under WinXP and Win2K for me.

Please have a look at BarleyBase,
http://barleypop.vrac.iastate.edu/BarleyBase/,  
the microarray database dedicated to Barley1 GeneChip data.



Lishuang Shen

BarleyBase
Iowa State University
Ames, Iowa 50010
Tel: (515)-294-8479 (Office)
Email: lshen at iastate.edu

-------------------------------------------------------
Message: 3
Date: Mon, 03 Nov 2003 10:27:08 -0500
From: "James MacDonald" <jmacdon at med.umich.edu>
Subject: Re: [BioC] CDF package needed for Barley chip
To: <ute.baumann at adelaide.edu.au>, <bioconductor at stat.math.ethz.ch>
Message-ID: <sfa62d96.090 at med-gwia-02a.med.umich.edu>
Content-Type: text/plain; charset=US-ASCII

In order to create this cdfenv, you will need to peruse the
instructions
for building packages under windows (I have to assume you are on
win32),
which can be found in the R for Windows FAQ, question 3.1.

Although relatively straightforward to do, getting your win32 box set
up for compiling packages can be a frustrating experience. If you
choose
to do so, make sure you follow the instructions on Brian Ripley's site
EXACTLY. The instructions are terse, but everything you need to know
is
there.

You will need to compile makecdfenv because there isn't a compiled
package yet, and once you have made the cdfenv, you will need to run
RCMD INSTALL to install it. This could easily take a while for you to
do
if you are not well versed with computers, so in the interim I am
sending you the envs directly. However, I would highly recommend you
take the time to be able to compile your own packages. It has made my
life much easier.

BioCore: I can contribute the envs if there is an interest.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "U. Baumann" <ute.baumann at adelaide.edu.au> 11/02/03 11:22PM >>>
Dear all,

Does anyone have a CDF package of the Barley1 Chip for R for Windows?
Or can
someone please create one or help me creating one. The original CDF
file can
be obtained at
http://www.affymetrix.com/support/technical/byproduct.affx?product=bar
ley1

or from me.

Regards,

Ute Baumann

----

Dr Ute Baumann
Australian Centre for Plant Functional Genomics
The University of Adelaide
PMB 1 Waite Campus
Glen Osmond 5064