Let's do $x[$n[$j]][$j] in bits:

  foreach my $j ($col_start .. $#column) {
    my $nIndex = $n[$j];

    $x[$nIndex][$j] = $column[$j];
    $x_tot[$j] += $x[$nIndex][$j];
    $n[$j]++;
  }
[download]

The 'uninitialized value' error can then be fix by:

  foreach my $j ($col_start .. $#column) {
    my $nIndex = $n[$j] // 0;

    $x[$nIndex][$j] = $column[$j];
    $x_tot[$j] += $x[$nIndex][$j];
    $n[$j]++;
  }
[download]