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revision 1.11, Sat Jun 5 15:38:44 2010 UTC revision 1.12, Mon Jun 7 17:01:08 2010 UTC
# Line 29  Line 29 
29  &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple");  &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple");
30  chdir $exp_ed;  chdir $exp_ed;
31    
32  &make_missing_probes("$exp_ed/peg.probe.table.no.multiple", "$exp_ed/probes", "$exp_ed/probe.no.match");  my $peg_probe_table = "$exp_ed/peg.probe.table.no.multiple";
33    my $probe_no_match = "$exp_ed/probe.no.match";
34    
35    &make_missing_probes($peg_probe_table, "$exp_ed/probes", $probe_no_match);
36    
37    &run("Rscript $FIG_Config::bin/RunRMA.R $peg_probe_table $probe_no_match $exp_ed/Experiments $exp_ed 2> $exp_ed/stderr.RMA");
38    
39    #&run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA");
40    
 &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA");  
41  &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters");  &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters");
42  &run("$FIG_Config::bin/make_coreg_conjectures_based_on_subsys  $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.subsys   2> $exp_ed/stderr.coregulated.subsys");  &run("$FIG_Config::bin/make_coreg_conjectures_based_on_subsys  $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.subsys   2> $exp_ed/stderr.coregulated.subsys");
43  &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets | filter_on_known $exp_ed/raw_data.tab > $exp_ed/merged.clusters");  &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets | filter_on_known $exp_ed/raw_data.tab > $exp_ed/merged.clusters");

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