def _read_ExpressionSet_RData(RData):
"""Read ExpressionSet RData to Rpy2 robjects.
RData: Path to the input RData file.
ExpressionSet must be the only object in the RData.
Return Rpy2's eSet object, assayData, featureData, phenotypeData.
"""
importr('Biobase')
rdata = r.load(RData)
eSet = r.get(rdata) # rpy2 ExpressionSet object (assumed)
assayData = r.assayData(eSet) # rpy2 environment object
fData = r.fData(eSet) # rpy2 DataFrame object
pData = r.pData(eSet) # rpy2 DataFrame object
return eSet, assayData, fData, pData
def estimateExpression(infiles, outfile):
'''estimate expression levels.'''
R.library("affy")
E.info("reading data")
raw_data = R.ReadAffy(infiles)
E.info("RMA normalization")
eset = R.rma(raw_data)
R.boxplot(raw_data)
R.boxplot(eset)
print R.as_list(R.assayData(eset))
def estimateExpression(infiles, outfile):
"""estimate expression levels."""
R.library("affy")
E.info("reading data")
raw_data = R.ReadAffy(infiles)
E.info("RMA normalization")
eset = R.rma(raw_data)
R.boxplot(raw_data)
R.boxplot(eset)
print R.as_list(R.assayData(eset))