Beispiel #1
0
def test_lowess():
    """
    Tests lowess normalization. 
    """
    counts_fname = utils.load_testdata("pasilla")
    # Consider only a subset of the samples
    samples = OrderedDict()
    samples["Untreated 1"] = "untreated1"
    samples["Untreated 2"] = "untreated2"
    exp_obj = experiment.Experiment(counts_fname, samples)
    pairs = [["untreated1", "untreated2"]]
    norm_df, unnorm_df = normalizers.norm_ma_lowess(exp_obj, pairs)
    print "\nLowess Testing:"
    print "--------------"
    print "Pre-normalized values: "
    print unnorm_df.head()
    print "Normalized counts: "
    print norm_df.head()
    # Compare LOWESS normalized to total counts
    pair = ["untreated1", "untreated2"]
    plot_utils.plot_fcs(norm_df, unnorm_df, pair, "lowess_test")
Beispiel #2
0
def test_lowess():
    """
    Tests lowess normalization. 
    """
    counts_fname = utils.load_testdata("pasilla")
    # Consider only a subset of the samples
    samples = OrderedDict()
    samples["Untreated 1"] = "untreated1"
    samples["Untreated 2"] = "untreated2"
    exp_obj = experiment.Experiment(counts_fname, samples)
    pairs = [["untreated1", "untreated2"]]
    norm_df, unnorm_df = normalizers.norm_ma_lowess(exp_obj, pairs)
    print("\nLowess Testing:")
    print("--------------")
    print("Pre-normalized values: ")
    print(unnorm_df.head())
    print("Normalized counts: ")
    print(norm_df.head())
    # Compare LOWESS normalized to total counts
    pair = ["untreated1", "untreated2"]
    plot_utils.plot_fcs(norm_df, unnorm_df, pair, "lowess_test")