What I am trying to do is to implement the Hierarchical Clustering algorithm with UPGMA (Average distance between clusters) and various distance metrics (Pearson, Manhattan).
The results required: plot of data in experiment space showing the clustering according to the various distance metrics and a text file with gene clustering using the notation: (A, ((B,C),D)) meaning B & C are closest and then D etc...
The code that I have compiles but I can't run it if you know what I am doing wrong please help. The code is below:
import java.io.*;
class Numbers
{
public static void Manhattan(double[][] a,double[][] b,int n,int n2)
{
int q=n2;
int c=n;
for(int m=0;m<q;m++)
{
for(int h=0;h<q;h++)
{
double d=0;
double d2=0;
for(int j=0;j<c;j++)
{
d2=a[m][j]-a[h][j];
if(d2<0)
d2=d2*-1;
d=d+d2;
}
b[m][h]=d;
}
}
}
public static void main(String[] args)
{
double x1=0;
double x2;
double x3;
double y;
double y1=0;
double y2=0;
double y3=0;
double z=0;
double z1=0;
double z2=0;
double z3=0;
double total=0;
/*x=x1;
y=x2;*/
z=3-2;
z1=0;
if(z1<0)
{
z1=z1*-1;
}
else
{
total=z1+z2+z3;
}
String[] s2=new String [9];
BufferedReader inFile;
try{
inFile=new BufferedReader(new FileReader("Data_Set_1.txt"));
String s=inFile.readLine();
for (int i=1;i<61;i++)
{
s2=s.split(" ");
}
}
catch(Exception e){}
System.out.println();
}
}
Below is the Data_Set_1.txt
Gene Number Gene Name Experiment 1 Experiment 2 Experiment 3
1 Y1 -9.30 5.65 -5.02
2 Y2 -4.10 5.68 0.56
3 Y3 4.75 0.11 2.86
4 Y4 -1.54 -10.01 -1.99
5 Y5 -6.29 5.62 -2.78
6 Y6 -13.02 1.31 1.61
7 Y7 -5.85 3.79 -6.56
8 Y8 -12.71 -0.45 0.62
9 Y9 -3.05 -12.65 -5.07
10 Y10 2.18 -5.82 -9.73
11 Y11 1.74 -0.99 -3.66
12 Y12 -7.88 0.93 -8.33
13 Y13 -6.34 -1.85 -4.00
14 Y14 -0.71 -2.64 -5.64
15 Y15 2.77 -4.16 -3.83
16 Y16 -0.25 0.58 0.77
17 Y17 2.52 -5.80 -8.80
18 Y18 5.53 -9.11 -1.92
19 Y19 6.63 2.53 7.94
20 Y20 -7.11 8.09 -6.47
21 Y21 -0.30 -6.18 -6.25
22 Y22 -0.33 4.58 -8.32
23 Y23 -2.39 1.44 3.94
24 Y24 7.70 9.39 4.73
25 Y25 4.89 -6.17 6.98
26 Y26 6.05 -6.54 -1.94
27 Y27 6.78 7.83 -7.72
28 Y28 4.86 2.31 2.33
29 Y29 6.93 3.95 10.61
30 Y30 0.04 -7.31 -1.49
31 Y31 -4.78 3.41 10.69
32 Y32 5.55 -6.48 -0.56
33 Y33 -3.18 -4.32 -3.32
34 Y34 3.67 -9.79 -13.03
35 Y35 -11.01 -3.69 -5.13
36 Y36 -2.24 -2.19 -12.74
37 Y37 8.84 2.10 1.28
38 Y38 0.69 7.11 -5.35
39 Y39 -9.19 -6.10 -11.01
40 Y40 2.37 6.58 2.67
41 Y41 6.40 6.03 3.58
42 Y42 -0.54 -1.32 -0.69
43 Y43 -0.45 0.01 -0.25
44 Y44 0.52 0.96 0.28
45 Y45 0.86 1.07 0.96
46 Y46 -0.47 -1.36 -0.81
47 Y47 -0.64 -1.47 -0.32
48 Y48 0.34 -0.47 0.46
49 Y49 -0.27 -0.62 -0.43
50 Y50 -0.49 -0.22 -0.01
51 Y51 -9.80 2.34 -5.95
52 Y52 6.74 -8.43 4.21
53 Y53 -7.60 -6.57 -5.13
54 Y54 -6.53 -2.55 -13.86
55 Y55 -3.82 7.12 -11.45
56 Y56 5.49 -7.60 0.40
57 Y57 6.95 -2.61 -5.14
58 Y58 0.21 -6.98 0.84
59 Y59 1.65 3.77 3.33
60 Y60 6.16 3.25 -14.31
I would appreciate greatly any help I get.
Linear Mode
