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Small cleanup.

This commit is contained in:
Truls Alexander Tangstad 2006-05-09 14:16:22 +00:00
parent 443b18cea6
commit 9ab1ebe687
1 changed files with 1 additions and 3 deletions
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4
workflows/affy_workflow.py
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@ -161,9 +161,7 @@ Example: Y-N, M-F""" % ", ".join(data.get_categories()))
rpy.r.assign("expr", affy.asarray()) rpy.r.assign("expr", affy.asarray())
silent_eval("fit <- lmFit(expr, design)") silent_eval("fit <- lmFit(expr, design)")
# FIXME: might be a case for code injection... silent_eval("contrast.matrix <- makeContrasts(%s, levels=design)" % response)
string = "contrast.matrix <- makeContrasts(%s, levels=design)" % response
silent_eval(string)
silent_eval("fit2 <- contrasts.fit(fit, contrast.matrix)") silent_eval("fit2 <- contrasts.fit(fit, contrast.matrix)")
silent_eval("fit2 <- eBayes(fit2)") silent_eval("fit2 <- eBayes(fit2)")
coeff = rpy.r("fit2$coefficients") coeff = rpy.r("fit2$coefficients")