Hi,

ok. I actually continue using my code as I feel more familiarize with it but did accordingly to how you advise me and I can come out with the output I want:

 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)
           {
           $ratio1 = sprintf( "%.4f%s", $$arr_ref2[$index1]/$$arr_ref1
+[$index1],"\t");     
            $variable1 .= $ratio1;

           } 

           for my $index2 (5..6)
           {
           $ratio2 = sprintf( "%.4f%s", $$arr_ref2[$index2]/$$arr_ref1
+[$index2],"\t");
           $variable2 .= $ratio2;
  
           }              
             #Calculate Average             
             @arrayint1 = split (/\t/,$variable1);                  
             $avg1 = &average (\@arrayint1);     
             #print OUT1 "\t$avg1";
               
             @arrayint2 = split (/\t/,$variable2);                  
             $avg2 = &average (\@arrayint2);     
             #print OUT1 "\t$avg2";
             
             #Calculate SD
             @arrayint1 = split (/\t/,$variable1);                  
             $std1 = &stdev(\@arrayint1);     
             #print OUT1 "\t$std1";
               
             @arrayint2 = split (/\t/,$variable2);                  
             $std2 = &stdev(\@arrayint2);     
             #print OUT1 "\t$std2";
             
             #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";

         } 
            }  

  sub average{
        my($data) = @_;
        if (not @$data) {
                die("Empty array\n");
        }
        my $total = 0;
        foreach (@$data) {
                $total += $_;
        }
        my $average = $total / @$data;
        return $average;
}
sub stdev{
        my($data) = @_;
        if(@$data == 1){
                return 0;
        }
        my $average = &average($data);
        my $sqtotal = 0;
        foreach(@$data) {
                $sqtotal += ($average-$_) ** 2;
        }
        my $std = ($sqtotal / (@$data-1)) ** 0.5;
        return $std;
}
[download]

so the output will be :

_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
.
.
[download]

So far so good. Phew! Thanks to your guidance! :)

My next question is, is it possible to actually filter the whole row based on the outputd(set condition)?

(not sure if it should be put into a new thread?)

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