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

From: John Maindonald <john.maindonald_at_anu.edu.au>
Date: Sat, 09 Apr 2011 18:17:21 +1000

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


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