[Bioc-devel] Package size limitation

hpages at fhcrc.org hpages at fhcrc.org
Fri Aug 1 19:25:14 CEST 2008

Hi Henrik,

Quoting Henrik Bengtsson <hb at stat.berkeley.edu>:
> Now to a trick: If you do want to distribute an AffyBatch object, have
> a look at your intensities.  If your chip type is a 3x3 pixel per
> probe array, and the Affymetrix image analysis (typically) took the
> 75% quantile (7:th ordered pixel), you will actually see only integer
> probe signals.  Note, this is not a rounding error but it just happens
> "by chance".  If this is the case with your data, you could create an
> object holding the signals as integers and not doubles without loosing
> anything.  That object would be roughly half the size.  I don't think
> compression algorithms can pick this up.

Yes they do:

   > xx <- sample(1000000L, 5000000, replace=TRUE)
   > typeof(xx)
   [1] "integer"
   > object.size(xx)
   [1] 20000040
   > yy <- as.double(xx)
   > typeof(yy)
   [1] "double"
   > object.size(yy)
   [1] 40000040
   > save(xx, file="xx.rda")
   > save(yy, file="yy.rda")

Then from the shell:

   hpages at lamprey:~> ls -lh *.rda
   -rw-r--r-- 1 hpages compbio 16M 2008-08-01 10:19 xx.rda
   -rw-r--r-- 1 hpages compbio 18M 2008-08-01 10:19 yy.rda


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