Something like this? 
use strict;
use warnings;
use List::Util qw(sum);

my %table;
while (defined(my $line = <DATA>)) {
    my @values = split(/\s+/, $line);
    push @{$table{$values[3]}}, \@values;
}

foreach my $key (sort keys %table) {

    my $avg_diff = sum(map { ($_->[5] / 1000) - ($_->[4] / 1000) } @{$
+table{$key}}) / @{$table{$key}};

    foreach my $array_ref (@{$table{$key}}) {
        if ($avg_diff >= 0.02) {
            print join("\t", @{$array_ref}), "\n";
        }
    }
}

__DATA__
chr1      15865      15915      cg13869341      908      913
chr1      18827      18877      cg14008030      688      776
chr1      29407      29457      cg12045430      43      70
chr1      29407      29457      cg12045430      43      88
chr1      29407      29457      cg12045430      43      16
chr1      29425      29475      cg20826792      57      70
chr1      29425      29475      cg20826792      57      88
chr1      29425      29475      cg20826792      57      16
chr1      29435      29485      cg00381604      33      70
chr1      29435      29485      cg00381604      33      88
chr1      29435      29485      cg00381604      33      16
chr1      68849      68899      cg20253340      560      593
chr1      69591      69641      cg21870274      791      809
chr1      91550      91600      cg03130891      55      84

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In reply to Re: compare values while value on other column remains the same by Anonymous Monk
in thread compare values while value on other column remains the same by linseyr

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