setNormalizationMethod {geneClassifiers} | R Documentation |
setNormalizationMethod
is to be called prior to running a classifier.
setNormalizationMethod(expressionSet, method, ...)
expressionSet |
An object of class |
method |
A character string indicating the normalization that was applied to the data.
Possible values are given by |
... |
see details. |
The FixedExpressionData
class forms together with the
ClassifierParameters
class the basis for input to the runClassifier
function. The data inside the FixedExpressionData
-class has to be stored as it is
right after normalization. This function may require some additional arguments:
isLog2Transformed = TRUE
Use this argument if the data already underwent a
log2transformation, as is common e.g. in case of MAS5.0 normalization.
targetValue = value
This is a MAS5.0 specific argument. It is the sample intensity
mean when the lowest and highest 2% of intensities are discarded. If only part of the original
expression set is given to this function, then this argument is required.
An object of class FixedExpressionData
Other workflow functions: getNormalizationMethod
,
runClassifier
,
showClassifierList
data(exampleMAS5) myData <- setNormalizationMethod(exampleMAS5, "MAS5.0",targetValue=500) results <- runClassifier('EMC92', myData) getScores( results ) getClassifications( results )