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Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it.

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Truls Alexander Tangstad
2006-05-05 14:43:53 +00:00
parent 97f56f66ac
commit 0db25f1dd7
4 changed files with 4 additions and 8 deletions
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2
workflows/affy_workflow.py
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@@ -203,7 +203,7 @@ class PCAFunction(workflow.Function):
dim_2, dim_1 = data.get_dim_names()
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.get_matrix())
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.asarray())
silent_eval("t = prcomp(t(m))")
# we make a unique name for component dimension

2
workflows/go_workflow.py
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@@ -236,7 +236,7 @@ class PCAFunction(workflow.Function):
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.get_matrix())
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.asarray())
silent_eval("t = prcomp(t(m))")
T_ids = map(str, range(1, rpy.r("dim(t$x)")[1]+1))