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Implemented Limma function for Affy workflow.

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Extended ScatterPlot to take two datasets and updated code using it.
This commit is contained in:
Truls Alexander Tangstad
2006-05-09 13:17:17 +00:00
parent 033d4d5333
commit 5b1af849dc
6 changed files with 144 additions and 24 deletions
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23
test/workflows/affy_workflowtest.py
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@@ -86,6 +86,29 @@ CEL\tsex\tage\tinfected
self.assertEquals(set(['F', 'M', 'I', 'N']), set(dataset.get_categories()))
def testGetFactors(self):
cel_data = """\
CEL\tsex\tage\tinfected
02-05-33\tF\t8\tI
02-05-34\tF\t9\tN
02-05-35\tM\t8\tI
"""
dataset = PhenotypeDataset(cel_data)
self.assertEquals(set(["sex", "infected"]), dataset.get_factors(["F", "I"]))
def testGetCategoryVariable(self):
"""Can get set/unset list for given category."""
cel_data = """\
CEL\tsex\tage\tinfected
02-05-33\tF\t8\tI
02-05-34\tF\t9\tN
02-05-35\tM\t8\tI
"""
dataset = PhenotypeDataset(cel_data)
self.assertEquals([1, 1, 0], dataset.get_category_variable("F"))
self.assertEquals([0, 0, 1], dataset.get_category_variable("M"))
self.assertEquals([1, 0, 1], dataset.get_category_variable("I"))
self.assertEquals([0, 1, 0], dataset.get_category_variable("N"))
if __name__=='__main__':