bioinformatics,
I am not exactly sure I understand. What I think you are looking for is for each "row" to consist of a single element from a list of arrays. This might be what you wanted. I tested it with dummy data.

#!/usr/bin/perl -w
use strict;
use Text::CSV;

my %data = (
    one   => [ qw(a b c d e f g h i j k) ],
    two   => [ qw(1 2 3 4 5 6 7 8) ],
    three => [ qw(john jacob jingle heimer smitz) ]
);

my @keys = sort keys %data;
my $max = 0;

for ( @keys ) {
    $max = @{$data{$_}} if @{$data{$_}} > $max;  
}

Excel(\@keys);

for my $index ( 0 .. $max ) {
    my @temp;
    for my $key ( @keys ) {
        push @temp, defined $data{$key}->[$index] ? $data{$key}->[$ind
+ex] : '';     
    }
    Excel(\@temp);
}

sub Excel {
    my $array = shift;
    my $csv = Text::CSV->new;
    if ( $csv->combine(@{$array}) ) {
        my $string = $csv->string;
        print $string, "\n";
    }
    else {
        my $err = $csv->error_input;
        print "combine() failed on argument: ", $err, "\n";
    }
}
[download]

Cheers - L~R

Update: Added Text::CSV stuff since it sounded like the output is going to Excel.