OK, now we're talking.

Assuming you want a result which is first the AFFX-BioB-xxx_at-identifier, followed by all signal-data which are connected to this identifier, I suggest:

• you drop the get_targets sub and all references to it.
• Then you change your sub get_signal to:

      while (@filename) {
          my $i;
          $file=shift @filename;
          use Cwd 'chdir';
          chdir "./data";
          open (FILE, "$file") or die;
          while (<FILE>) {
              next while $i++ <= 14;
              (my $id, undef, undef, my $signal, undef, undef)=split(/\t
  +/);
          push @{$outputdata{$id}}, $signal;
          }
          close (FILE);
      }
  [download]

  After having run this sub over all your files you will find in %outputdata a nicely ordered (per identifier) structure of your signal-data.
• "Printing this datastructure goes as follows:

  for $id (keys %outputdata) {
      print "$id:\t",(join("\t",@{$outputdata{$id}})),"\n";
  }
  [download]

  Of course you can print it to a filehandle. This is a format which is suitable to be imported in a database or a spreadsheet.

The "magic" of using references to anonymous arrays may perhaps be a bit too deep for someone who is just starting to program, but if you read Chapters 8 and 9 of the Camel book a few times and study the examples given, much will become clearer.

CountZero

"If you have four groups working on a compiler, you'll get a 4-pass compiler." - Conway's Law