Yes to the following:
•You have multiple, tab-delimited files
•The first line of each file contains column headers
•Each file may have a different number of columns


##</code><code>##

e.g.
first file.txt:

ID  dataS01R1  dataS01R2  dataS02R1  dataS02R2  Links
M45  345.2      536        876.12      873       http://..
M34  836        893        829         83.234    
M72  873        123        342.36      837       
M98  452        934        1237        938       http://..

===================================================
Calculation:
row2/row2, row3/row2, row4/row2...row3400/row2 
row2/row3, row3/row3, row4/row3 ... row3400/row3
row2/row4, row3/row4 ...row3400/row4

E.g dataS01R1
become:
ID  dataS01R1             ..dataS01R02...  Links
M45  1      (345.2/345.2)                  http://..
M34  2.42   (836/345.2)      
M72  2.52   (873/345.2)      
M98  1.309  (452/345.2)                    http://..
M45  0.41   (345.2/836)                    http://..
M34  1      (836/836)      
M72  1.04   (873/836)      
M98  0.54   (452/836)                      http://..
.
.   (loop through rows as denominator)
.



##</code><code>##

 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...";