Welcome to PerlMonks, GeneGeek!

This:

my $rep_sample = $data->{$rep_label}  {'Samples'}{$dye};
[download]

...shouldn't have the whitespace in it. perl ignores whitespace, but it should be:

my $rep_sample = $data->{$rep_label}{'Samples'}{$dye};
[download]

That piece of code is looking deep into a hash (reference) of hashes, of hashes.

Parent has been updated with full code... What we need to see is the code that processes the data file and extracts the information into the hash.