Package net.sf.basedb.util.ma
Class MACalculator
- java.lang.Object
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- net.sf.basedb.util.ma.MACalculator
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- Direct Known Subclasses:
Log10MACalculator
,Log2MACalculator
public class MACalculator extends Object
Calculates M and A values for 2-channel data. For "normal" intensity values M and A are defined as follows: M = log2(ch1/ch2) A = log10(ch*ch2)/2 Channel intensity corrections are used to calculate new values for channel 1 and 2. For corrections that use M+A values the corrections are usually calculated in log2-space and the resulting equations are: log2(newCh1) = log2(oldCh1) - factor log2(newCh2) = log2(oldCh2) + factor Source data that has been transformed (eg. log2-transformed) must use different equations to get the correct results.- Since:
- 3.2.4
- Author:
- nicklas
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Field Summary
Fields Modifier and Type Field Description (package private) static double
INV_LN10x2
(package private) static double
INV_LN2
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Constructor Summary
Constructors Constructor Description MACalculator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
correct(double ch1, double ch2, double factor)
Apply a correction factor to the ch1 and ch2 intensity values.double[]
MA(double ch1, double ch2)
Calculate the M and A values from the ch1 and ch2 intensity values.
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Method Detail
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MA
public double[] MA(double ch1, double ch2)
Calculate the M and A values from the ch1 and ch2 intensity values. See class description for information about the definitions of M and A.- Returns:
- An array with [0] = M, [1] = A
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correct
public double[] correct(double ch1, double ch2, double factor)
Apply a correction factor to the ch1 and ch2 intensity values.- Returns:
- An array with [0] = newCh1, [1] = newCh2
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