Or, you could do it the old-fashioned way...

opendir(DATADIR, "files/$department") or die "Invalid directory!";
@duplicate = readdir(DATADIR);
closedir(DATADIR);

foreach $item (@duplicate) {
   if ($item eq "files/$department/$number.txt") {
      $go_sub = 'yes';
      last;
   }
}
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I have usually used glob() myself, but I read recently that it's not the best way to do it, that it has some quirks on different platforms. As for what those quirks are, I haven't a clue.

Update: However, in reading your code, it looks as though you may be simply trying to verify the presence of a file in that directory... perhaps you just want the -e operator, to see if the file exists:

$go_sub = "yes" if -e "files/$department/$number.txt";
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