net.sf.basedb.util.ma
Class MACalculator
java.lang.Object
net.sf.basedb.util.ma.MACalculator
- 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
Field Summary |
(package private) static double |
INV_LN10x2
|
(package private) static double |
INV_LN2
|
Method Summary |
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. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
INV_LN2
static final double INV_LN2
INV_LN10x2
static final double INV_LN10x2
MACalculator
public MACalculator()
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
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