use Data::Dumper;

my $header = <DATA>;
my @cols_h = split /\t/, $header;

my @data;

while (<DATA>)
{
    chomp;
    my @info = split /\t/;
    push @data, \@info;
}

# uncomment this to see the data we have so far.
#print Dumper(\@data);

foreach (@data)
{
    my $avg = ($_->[2] + $_->[3]) / 2;
    push @$_, $avg
}

# uncomment this to see the data we have so far.
#print Dumper(\@data);

# at this point, each @data is an array of arrays.
# Each of the arrays contained in @data is "anonymous" (unnamed).
# These anonymous arrays have the four columns (0-3), and a fifth column
# which is an average of columns 2 and 3 (zero-based).

__DATA__
ID_REF	IDENTIFIER	GSM29783	GSM29784
31307_at	L17325	77	788
31308_at	L17330	-777	-877
31309_r_at	U50277	7	8
31310_at	X52009	-7777	-887
31311_at	X61070	77777	88