It would be easier to help you if you posted actual code rather than the vague description "and comparing the $m ==$m1 and also /(\w+)(a|b|c). and comparing the $1 of one sample with the other".

It's only a guess but maybe something like the following would do what you want.

use strict;
use warnings;

my @samples = qw(
    PD4005a
    PD4005b
    PD4005c
    WGA_PD4005a
    WGA_PD4005b
    WGA_PD4005c
    DIFFERENT
);

foreach my $s1 (@samples) {
    foreach my $s2 (@samples) {
        next if(compare($s1,$s2));
        print "$s1 - $s2\n";
    }
}

sub compare {
    my ($s1, $s2) = @_;

    if($s1 =~ m/^(WGA_)?PD(\d+)[abc]$/) {
        my $n1 = $2;
        if($s2 =~ m/^(WGA_)?PD(\d+)[abc]$/) {
            return($n1 == $2);
        }
    }
    return(0);
}
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