Could have sworn I fixed a bug but found it here. I took the averaging out of the DataAnalyser.java class and gave it it's own class with a main method specially for performing this calculation. A lot neater than before and easy to see what is going on.

AverageData.java

/*
  	AverageData.java 
		=============
		
    This is a program to help with data analysis.
    You can open a one column array and average all the data points.
    File must be in the format where the first line gives its length
    eg.
    length = 30
    x_1
    x_2
    .
    .
    .
    .
    X+n
    
    
    Copyright (C) 2013  Magdalen Berns

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Scanner;

public class AverageData {

    public static void main(String[] args) throws IOException {
  
  		  System.out.printf("Please type the name of the data file you wish to average. \n"); 
				String choice= IOUtil.getFileName();
 				if(!choice.equals(null)){
						Scanner scan = new Scanner(new BufferedReader(new FileReader(choice)));
						int length = IOUtil.skipToInt(scan);
						double[] data = PlotReader.data1Column(scan,length);
						double mean = StatsUtil.mean(data);
						System.out.printf("Mean value %g \n", mean); 
						System.out.printf("std Dev value %g \n", Math.sqrt(StatsUtil.variance(data,mean))); 
						System.exit(0);
				}
		}
}