Hi anonymous monk, yes I'm still finding this confusing.

Well hold onto your pants :)

You mentioned it is confusing $dataset for a hashref.

Look at the @beef equivalent example, it is this line that dies with Can't use an undefined value as an ARRAY reference

 my @beef = @{ $dataset->{ $col[0] } };
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my $key  = $col[0] ;
my $meat = $dataset->{ $key };
my @beef = @{ $meat };
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The problem is, $key is not in $dataset, so $meat is undef

Since meat is undef, trying to treat $meat as an array by de-referencing it, triggers a warning if you have warnings on, and triggers an error, if you have strict on.

## no warnings or errors
$ perl -e "print @{ undef() }; print 6"
6

## a warning is issued, but 6 still gets printed
$ perl -we "print @{ undef() }
Use of uninitialized value in array dereference at -e line 1.
6

## with strict the warning is fatal, 6 not printed cause program died
$ perl -Mstrict -we "print @{ undef() }
Can't use an undefined value as an ARRAY reference at -e line 1.
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To avoid this error, you might add

next unless $meat;
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Lets take apart a simpler example, one that builds @data

Thanks for the detailed post. I'm still having problems with the "Use of uninitialized value in array element" error. I adjusted the code, however I'm not sure where I need to insert the equivalent of the

next unless $meat;

I can get it to work by commenting out use strict;

##!/usr/bin/perl
#22/06/2011

use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data;
my @col;
my $dataset;
my @fields;
my %out;
my $Hashref;
my $fileCount;
my @out; 

open INFILE, "<Primer-Rev1" or die $!;
open my $outfh, '>', "outputfile.txt" or die $!;

    for my $nr (1..2) {
     for my $line (read_file('Primer-For'.$nr)) {
      my @col = split(/\t/,$line);


      push @{$data[$nr - 1]->{shift(@col)}},\@col;
     }
    }


while (<INFILE>){

        @col = split(/\t+/, $_);
        chomp (@col);
         my ($header, $length, $tm, $sequence) = @col[0..3];

        # expecting file3 line in @col

        my @results = ( $col[1], $col[2] );

#print Dumper (\@results)


for my $dataset (@data) {
    my @out = push @{
    $data[ $fileCount ]->{
        shift @col
    }
},  \@col;


#print Dumper (\@data);
#}

    @out = 
        sort {
            my $diff_a = $col[2] - $a->[1];
            $diff_a *= -1 if $diff_a < 0;
            my $diff_b = $col[2] - $b->[1];
            $diff_b *= -1 if $diff_b < 0;
            $diff_a <=> $diff_b;
          }   @out;

print Dumper (\@out);

    push @results, $out[0]->[2];
}


#foreach (@results){
#    print $_."\n"}

}
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however I'm not sure where I need to insert the equivalent of the

Next line, right after you initialize $meat

    push @{
    $data[ $fileCount ]->{
        shift @col
    }
},  \@col;
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Wait a minute, why did you copy that?