You can add a check that the second element has some value. 
perl -wle '$a[1]=[1];print $a[1]->[0];if($a[1]->[1]){print$a[1]->[1]}'
r
perl -wle '$a[1]=[1,2];print$a[1]->[0];if($a[1]->[1]){print$a[1]->[1]}
+'
r
l

[download]
something like this should do it in your code 
for ( my $i = 0 ; $i < scalar @results ; $i++ ) {
        if ( $results[$i]->[0] eq $disease_name_pocus[0] ) {
            next unless $results[$i]->[1];
            if ( $results[$i]->[1] ne $results[ ( $i + 1 ) ]->[1] ) {
                print MARKER "$results[$i]->[1]\t$results[$i]->[4]\n";
            }
        }

[download]

Cheers,
Random.

In reply to Re: use of uninitialized value in string ne by Random_Walk
in thread use of uninitialized value in string ne by BioGeek

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