if($first)
    {
        #if this is the first file, find the column locations
        my $firstline = <CURINFILE>;        #read in the header line
        chomp $firstline;
        my @columns = split(/\t/, $firstline);
        
        my $columncount = 0;
      
        while($columncount <= $#columns && !($columns[$columncount] =~ /ID/))
        {
            $columncount++;
        }
        $ID= $columncount;
        
            while($columncount <= $#columns && !(($columns[$columncount] =~ /_dataS(\d+)R/) ))
        {
            $columncount++;
        }
        $intensitydata = $columncount;   
             		       
      #read in the remainder of the file
        while(<CURINFILE>)
        {
            #add the id, intensity values to an array
            chomp $_;
            my @templine = split(/\t/,$_);
            my @tempratio = ();
            push(@tempratio, $templine[$ID]);
            push(@tempratio, $templine[$intensitydata]);
            
                           
        print "\nWriting output...";