A memory error occurs when running FIRMA

What steps will reproduce the problem?
1. Run FIRMA on a 32 bit installation of Python with multiple experimental 
groups.

What is the expected output? What do you see instead?
Normally AltAnalyze should finish it's run but instead, a window appears 
indicating an unexpected error has occurred.

{{{
Calculating FIRMA scores (please be patient)...
Importing probe-to-probeset annotations (please be patient)...
Traceback (most recent call last):
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 3994, in AltAnalyzeSetup
    StatusWindow(root,expr_var, alt_var, goelite_var, additional_var, exp_file_location_db)
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 3641, in __init__
    sys.stdout = status; root.after(100, AltAnalyzeMain(expr_var, alt_var, goelite_var, additional_var, exp_file_location_db, root))
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 4368, in AltAnalyzeMain
    summary_results_db, aspire_output_gene_list, number_events_analyzed = RunAltAnalyze()
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 3598, in RunAltAnalyze
    summary_results_db, summary_results_db2, aspire_output, aspire_output_gene, number_events_analyzed = splicingAnalysisAlgorithms(relative_splicing_ratio,adj_fold_dbase,dataset_name,gene_expression_diff_db,exon_db,ex_db,si_db,dataset_dir)
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 1446, in splicingAnalysisAlgorithms
    splice_event_list, p_value_call, permute_p_values, excluded_probeset_db = FIRMAanalysis(fold_dbase)
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 2460, in FIRMAanalysis
    probe_probeset_db = importProbeToProbesets(fold_dbase); global firma_scores; firma_scores = {}
  File "G:\My_Elements\AltAnalyze_Latest\AltAnalyze_v1164release\AltAnalyze_v1164release\AltAnalyze.py", line 2422, in importProbeToProbesets
    for probe in probeset_probe_db[probeset]: probe_probeset_db[probe] = probeset
MemoryError
}}}
Original issue reported on code.google.com by nsalomo...@gmail.com on 19 Nov 2010 at 6:09
venkatmi / altanalyze

A memory error occurs when running FIRMA #2
