Re-added normalization to Medulloblastoma (needed in examples)

mims-harvard · Mar 17, 2015 · 91fb41c · 91fb41c
1 parent 1afe274
commit 91fb41c
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/docs/source/code/usage.py b/docs/source/code/usage.py
@@ -2,7 +2,7 @@
 
 V = nimfa.examples.medulloblastoma.read(normalize=True)
 
-lsnmf = nimfa.Lsnmf(V, seed='random_c', rank=50, max_iter=100)
+lsnmf = nimfa.Lsnmf(V, seed='random_vcol', rank=50, max_iter=100)
 lsnmf_fit = lsnmf()
 
 print('Rss: %5.4f' % lsnmf_fit.fit.rss())

diff --git a/nimfa/examples/medulloblastoma.py b/nimfa/examples/medulloblastoma.py
@@ -182,7 +182,7 @@ def reorder(C):
     return C[:, ivl][ivl, :]
 
 
-def read():
+def read(normalize=False):
     """
     Read the medulloblastoma gene expression data. The matrix's shape is 5893 (genes) x 34 (samples). 
     It contains only positive data.
@@ -191,6 +191,8 @@ def read():
     """
     fname = join(dirname(dirname(abspath(__file__))), 'datasets', 'Medulloblastoma',  'Medulloblastoma_data.txt')
     V = np.loadtxt(fname)
+    if normalize:
+        V = (V - V.min()) / (V.max() - V.min())
     return V