Was reading a thread about exactly this on Briskoda about an Octavia.
First of all, check the LED in the door -- if the alarm system is OK, it will flash rapidly for a couple of seconds and then settle down to a regular flash after switching the alarm on. If there is a fault, then the LED flashes rapidly for 2 seconds, stays on constant for 30 seconds, and then goes into the slow flash mode.
Secondly, get a scan with VAGCOM -- if the alarm siren is down, you'll probably get a fault code stating that there is no communication between the siren and the alarm
This indicates a faulty siren, and in the case of the Octavia, is around £90 from the dealer to replace.
Mike