[BioRuby] bioruby-testing-central on github
Pjotr Prins
pjotr2008 at thebird.nl
Sat Jun 14 14:07:56 UTC 2008
I have kicked off including support for microarrays in Bioruby with an
Affymetrix CEL file reader (which is based on Ben Bolstad's Affyio,
part of R/Bioconductor). The mapping is done in biolib
(http://biolib.open-bio.org/). Bioruby sources are on:
http://github.com/pjotrp/bioruby-testing-central/commit/5a32ff510208228b61483ee683d386ccbc3d87f2
Simple file loading works. E.g.
ARGV.each do | fn |
array = Bio::Microarray::Affy.new('GSM11002.CEL.gz')
(0..20).each do | i |
print array.intensity(i),", "
end
end
Next step is probe(set) mapping and support for regular tab delimited files and
CSV's (bit like read.table in R).
If anyone is interested in participating...
Pj.
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