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revision 1.12, Mon Jun 7 17:01:08 2010 UTC revision 1.13, Tue Jun 15 12:57:54 2010 UTC
# Line 45  Line 45 
45  &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table $exp_ed/raw_data.tab > $exp_ed/probes.always.on");  &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table $exp_ed/raw_data.tab > $exp_ed/probes.always.on");
46  &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");  &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on");
47  &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");  &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R");
48  &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters");  
49    # You need to compute a bunch of other things before the atomic regulons (update PCs, etc.)
50    #&run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters");
51  &run("$FIG_Config::bin/compute_atomic_regulons $genome");  &run("$FIG_Config::bin/compute_atomic_regulons $genome");
52    
53  sub make_missing_probes  sub make_missing_probes

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