The humming is most commonly caused by the magnetic field from the coils causing the iron core of the transformer to change dimensions--as it does so, it is vibrating, hence the noise. To some extent, all power transformers vibrate this way, although most are designed so that the vibration is minimized and sufficiently damped. If the noise is not too objectionable, you should just ignore it--there is probably not anything wrong with the transformer such that it will get worse. In any case contact the manufacturer if you can about this issue to see if it really is a manufacturing defect that they will address.
Someone above mentioned checking the bolts that hold the transformer down to the chassis. This is a very good first step. If they are loose, the vibration from the transformer might be made worse by the poor coupling to the chassis. If you are not experienced with tube gear, have someone who is experienced go under the hood because there may be high voltage stored in the capacitors that you don't want discharged through your body (amps can shock even when unplugged).
Good luck.