From john.maindonald at anu.edu.au  Sat Apr  9 10:17:21 2011
From: john.maindonald at anu.edu.au (John Maindonald)
Date: Sat, 9 Apr 2011 18:17:21 +1000
Subject: [Rd] Compression of largish expression array files in the
	DAAGbio/inst/doc directory?
In-Reply-To: <alpine.LFD.2.02.1104090748410.21478@gannet.stats.ox.ac.uk>
References: <51284363-243E-40B3-933A-B28F05986CBD@anu.edu.au>
	<alpine.LFD.2.02.1104090748410.21478@gannet.stats.ox.ac.uk>
Message-ID: <D8631AAC-09D4-4995-92BF-CF9A0F9D93D0@anu.edu.au>

Thanks.  That seems to work.

John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm

On 09/04/2011, at 4:58 PM, Prof Brian Ripley wrote:

> As far as I can see read.maimages is built on top of R's own file-reading facilties, and they all read compressed (but not zipped) files as from R 2.10.0.
> 
> So simply use
> 
> gzip -9 coral55?.spot
> 
> and rename the files back to *.spot.
> 
> If you need more compression, use xz -9e.  (You can also do this in R: readLines() on the file, writeLines() using gzfile or xzfile.)
> 
> You will need to make the package 'Depends: R (>= 2.10)'.
> 
> On Sat, 9 Apr 2011, John Maindonald wrote:
> 
>> The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that
>> are around 0.85 MB each.  It would be useful to be able to zip then, but that
>> as matters stand interferes with the use of the Sweave file that uses them to
>> demonstrate input of expression array data that is in the "spot" format.  They
>> do not automatically get unzipped when required.  I have checked that
>> read.maimages (in limma) does not, unless I have missed something, have
>> an option for reading zipped files.  Is there any way to get around this without
>> substantially complicating the exposition in marray-notes.pdf (also in the
>> inst/doc subdirectory)?
>> 
>> John Maindonald             email: john.maindonald at anu.edu.au
>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>> Centre for Mathematics & Its Applications, Room 1194,
>> John Dedman Mathematical Sciences Building (Building 27)
>> Australian National University, Canberra ACT 0200.
>> http://www.maths.anu.edu.au/~johnm
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?
John Maindonald