Here's a simple example of averaging columns of data, with your constraints thrown in (ignore and convert undefined and '-1' data):

my @sum;
my @num;
while (<DATA>) {
  my @data = split;
  $_ = (defined and $_ != -1)? $_ : '-' for @data;
  $sum[$_]+=$data[$_], $num[$_]++
    for grep { $data[$_] ne '-' } 0..$#data
}
print "@{[map { $sum[$_]/$num[$_] } 0..$#sum]}\n";

__DATA__
1 2 3 4
2 3 4 5
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