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java.lang.Objecthalo.normalization.Normalization
public abstract class Normalization
Provides methods for normalization and retrieving of correction factors
Field Summary | |
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static int |
UNDEF
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Constructor Summary | |
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Normalization()
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Method Summary | |
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abstract CorrectionFactors |
calculateCorrectionFactors()
calculates correction factors via normalization methods |
CorrectionFactors |
calculateCorrectionFactors(int replicate)
Calculates the correction factors for a certain replicate |
double[] |
calculateQualityControl(Data data,
boolean histogram)
Calculates the array containing the quality control values; these are calculated as distance from the normalization line |
void |
generateHistogram(double[] pqs,
double max)
Uses the PQS data and generates a histogram from it |
double |
getAlpha()
Returns the factor alpha from normalization |
double |
getBeta()
Returns the factor beta from normalization |
CorrectionFactors |
getCorr()
Returns the correction factors |
double |
getPqsMax()
Returns the highest value of the probe set quality scores |
int |
getReplicate()
Returns the replicate for calculation |
void |
setCorr(CorrectionFactors corr)
Sets the correction factors |
void |
setReplicate(int replicate)
Sets the replicate for calculation |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int UNDEF
Constructor Detail |
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public Normalization()
Method Detail |
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public abstract CorrectionFactors calculateCorrectionFactors()
public CorrectionFactors calculateCorrectionFactors(int replicate)
replicate
- The replicate for which the correction factors will be calculated
public double[] calculateQualityControl(Data data, boolean histogram)
data
- The data object containing the RNA valueshistogram
- TRUE if a histogram should be created for the quality scores, FALSE otherwise
public void generateHistogram(double[] pqs, double max)
pqs
- The probe-set quality control valuesmax
- The maximum value among these (for definition of the x-range)public void setCorr(CorrectionFactors corr)
corr
- The correction factorspublic void setReplicate(int replicate)
replicate
- The replicate for calculationpublic double getAlpha()
public double getBeta()
public CorrectionFactors getCorr()
public double getPqsMax()
public int getReplicate()
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