How did you do it? Unless you post code we can't tell what went wrong. Works fine for me

my @one = split /,/, '1,2,3,4,5,6';
my @two = split /,/, '2,9,8,4,7,6';
my @result;
for my $i ( 0 .. $#one ) {
    push @result, $one[$i] - $two[$i];
}
my $result = join ',', @result;
print $result, "\n";

__END__
-1,-7,-5,0,-2,0
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Update: As suggested by j1n3l0

use List::MoreUtils qw(pairwise);

my @one = split /,/, '1,2,3,4,5,6';
my @two = split /,/, '2,9,8,4,7,6';

our ($a, $b);  # keep warnings happy
my $result = join ',', pairwise { $a - $b } @one, @two;
[download]