When you 'compare variables', you compare their values. undef means that there is no useful value to compare.

Still, it's a warning, not an error. Look at the following example. It's not something very useful, but it shows that if you really want to, you CAN compare undef.

#!/usr/bin/perl
use warnings;
use v5.14;

{
  no warnings 'uninitialized';
  if ('ssd' ne undef) {
    say "The strings are not equal";
  }
}

{
  no warnings 'uninitialized';
  if ('' eq undef) {
    say "The strings seem equal";
  }
}
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Output:

The strings are not equal
The strings seem equal
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Edit: updated for clarity, added the example