hello perlbird and welcome to the monastery!

I do not know what reshape2 has to offer, but your immediate request would be a fairly simple data manipulation exercise. Along with examples in previous reply.

#!usr/bin/perl

use warnings;
use strict;

my %genetable;

while(<DATA>){
chomp;
next if /^#/;
my ($genekey, $samplevalue ) = split /\t/;
push @{ $genetable{$genekey} }, $samplevalue;
}

print map { "$_ @{$genetable{$_}}\n" } sort keys %genetable;

exit 0;
__END__
#omitted the header row
gene_A    sample_1
gene_B    sample_1
gene_C    sample_1
gene_B    sample_2
gene_C    sample_2
gene_A    sample_3
[download]

--------
gene_A sample_1 sample_3
gene_B sample_1 sample_2
gene_C sample_1 sample_2
[download]