Package ubic.basecode.math

Class TestMatrixNormalizer

java.lang.Object

ubic.basecode.math.TestMatrixNormalizer

public class TestMatrixNormalizer
extends Object

Author:

paul

Constructor Summary

Constructors

Constructor	Description
TestMatrixNormalizer()

Method Summary

Modifier and Type	Method	Description
void	testQuantileNormalize()	mm<-read.table("testdata.txt", header=T, row.names=1) library(preprocessCore) rr<-normalize.quantiles(as.matrix(mm)) rr[3,5] [1] 29860.93 > rr[13,5] [1] 466.7833 > rr[3,12] [1] 31620.79 > rr[4,10] [1] 1071.525 > rr[6,7] [1] 288.925 >
void	testQuantileNormalizeWithMissing()	Note that we do this differnetly than the Bioconductor implementation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestMatrixNormalizer

public TestMatrixNormalizer()

Method Detail

testQuantileNormalize

public void testQuantileNormalize()
                           throws Exception

 mm<-read.table("testdata.txt", header=T, row.names=1)
 library(preprocessCore)

 rr<-normalize.quantiles(as.matrix(mm))
  rr[3,5]
 [1] 29860.93
 > rr[13,5]
 [1] 466.7833
 > rr[3,12]
 [1] 31620.79
 > rr[4,10]
 [1] 1071.525
 > rr[6,7]
 [1] 288.925
 >

 

Throws:

Exception

testQuantileNormalizeWithMissing

public void testQuantileNormalizeWithMissing()
                                      throws Exception

Note that we do this differnetly than the Bioconductor implementation. For what it is worth here are the values they get

 dm<-read.delim("testdatamissing.txt", row.names=1, header=T)
     rr<-normalize.quantiles(as.matrix(dm))
 >  rr[3,5]
 [1] 30458.47
 > rr[13,5]
 [1] 737.1687
 > rr[3,12]
 [1] NA
 > rr[4,10]
 [1] 1187.655
 > rr[6,7]
 [1] 570.0667

 

Throws:

Exception