Instead, it print out only the last column:

so I change to this line by adding the "." to join the 6 columns together and I get weird output like this:

Would this do what you want?

my @ratio = map { sprintf '%.4f', $numerator[$_]/$denominator[$_] } 3.
+.8;
my $variable1 = join "\t", @ratio;
[download]

I know its got to do with the placement of the $variable1 .= "$ratio1"; ...but I have simply no idea how to go on and correct from there.

Sounds like you're not Coping with Scoping (tutorial and diagnosis)

If you can post more than a a fragment, something I can run (like your current short self contained program), I can explain what is going on

Hi, ok. Here's my actual code:

while(<CURINFILE>)
{
 push @full_data , [split] while (<CURINFILE>);
 for $arr_ref1 (@full_data) 
 {
  for $arr_ref2(@full_data)
  {
   print OUT1 "$$arr_ref1[0]\t$$arr_ref1[1]\t$$arr_ref1[2]\t\t"; #prin
+t first three columns of input data into textfile
        
    $firstend = $firstinput + 2;
    $start2 = $firstend + 1;
    $secondend = $firstend + $secondinput;
        
    for my $index1 (3..$firstend)#column 4 to end of group 1 column
    {
     $ratio1 = sprintf( "%.4f%s", $$arr_ref2[$index1]/$$arr_ref1[$inde
+x1],"\t");
     print OUT1 "$ratio1";
           
     #$variable1 .= "$ratio1"; #attempting to store values in $variabl
+e1 
             
     } 

      for my $index2 ($start2..$secondend)#start of group 2 column to 
+end)
      {
      $ratio2 = sprintf( "%.4f%s", $$arr_ref2[$index2]/$$arr_ref1[$ind
+ex2],"\t");
      print OUT1 "$ratio2";  
      #$variable2 .= "$ratio2"; #attempting to store values in $variab
+le1            
           }  
     print OUT1 "\n"; #print next line after one loop
    
      } # finish one loop of one ID

}
[download]

$arr_ref1(@full_data)and $arr_ref2(@full_data) refer to the same input of data from D to the end of data. Input DATA (Column letter is just to indicate my data)

A: ID
B, C (time)
C to E: Group 1
F to H: Group 2
# Calculation is taking the ratio of each row per column

_Input DATA_
A    B    C    D    E    F    G    H
M11 0.1   10   24  56   77   98   72
M12 0.3   13   44  23   45   56   11
M13 0.4   54   23  11   25   67   91
[download]

What my code on top does is to output this:

_OUTPUT DATA_
A    B    C    D    E    F    G    H    I
M11 0.1   10        1    1    1    1    1
M12 0.3   13        1.83 0.41 0.58 0.57 0.15
M13 0.4   54        0.95 0.19 0.32 0.68 1.26
.
.
.
[download]

Right now, I do not want to print the output out into textfile because I have huge dataset. So I am attempting to take output of the column E to I and put into variable and then be used to calculate the average by each group and row. That is why I put two groups (for loop) separately. After which, the data will be filtered and print out the desired output.

Hence, I add the $variable1 and $variable2 to join the values of each cell together. But the output become like this:

_OUTPUT DATA_
A    B    C    D    E    F    G    H    I     J   K
M11 0.1   10        1    1    1        
M11 0.1   10        1    1    1   1.83  0.95  
M11 0.1   10        1    1    1   1.83  0.95  1  0.41 
M11 0.1   10        1    1    1   1.83  0.95  1  0.41
.
.
.
[download]

I am really stuck here. Thanks for your patience in guiding me so far!

Well, thats not what I had in mind :)

Can you describe/explain what this loop does in one sentence? Your explanation will help me write a response you can understand (hopefully)

        for $arr_ref1 ( @full_data ) {
            for $arr_ref2 ( @full_data ) {
            }
           }
[download]