.
.
.

 while(<CURINFILE>)
    {
    push @full_data , [split] while (<CURINFILE>);
    for $arr_ref1 (@full_data)
    {
     for $arr_ref2(@full_data)  
     {
     $variable1 = '';
     $variable2='';
     for my $index1 (3..4) #first group
     {
     $ratio1 = ($$arr_ref2[$index1]/$$arr_ref1[$index1],"\t");     
     $variable1 .= $ratio1; #join column by column
     } 
     for my $index2 (5..6) #second group
     {
     $ratio2 = ($$arr_ref2[$index2]/$$arr_ref1[$index2],"\t");
     $variable2 .= $ratio2; #join column by column
     }              
   #Calculate Average             
   @arrayint1 = split (/\t/,$variable1);                  
   $avg1 = &average (\@arrayint1);     
               
   @arrayint2 = split (/\t/,$variable2);                  
   $avg2 = &average (\@arrayint2);     
             
   #Calculate SD
   @arrayint1 = split (/\t/,$variable1);                  
   $std1 = &stdev(\@arrayint1);     
               
   @arrayint2 = split (/\t/,$variable2);                  
   $std2 = &stdev(\@arrayint2);     
              
   #Calculate CV
   $cv1 = $std1/$avg1;
   $cv2 = $std2/$avg2;
           
   my $outputa = "$$arr_ref1[0]";  
   my $outputb = "$variable1\t$variable2\t";
   my $outputc = "\t$avg1\t$avg2";
   my $outputd = "\t$cv1\t$cv2";
                          
 ###### print everything out #####################

      my $key = "$outputa"."$outputb". "$outputc"."outputd";
      print OUT1 $key;
      print OUT1 "\n";
 } 
}  
.
(average and SD codes)
.

##</code><code>##

_OUTPUT_
M446T27    1     1     1     1        1     1      0   0 
M446T27 1.75  2.66  1.80  2.16     2.20  1.98  0.29 0.12
M446T27 1.00  1.64  0.99  1.09     1.32  1.04  0.34 0.06
.
.