I know this has been done to death on the LOC but it's not in the 'how to' section, and I had to trawl through the net trying the hundreds of different procedures that people had posted before I found the ones that worked for me. So here they are. I found that the timings are crucial and that it helps if you read them through several times before you start. Also if someone reads them to you whilst you do the work it may be a little easier.
I only had one Master key (3 buttons, Lock, Unlock and boot) one Sub key (2 buttons, Lock and Unlock) when I bought my GS. So I bought a used Lexus RX Master key from eBay and a blank, empty shell Master key. I had the blank blade cut to match mine and put the RX electronics it. Obviously then the key turns the door locks but the remote buttons don't work and the engine will only spin over and not start.
It's important to have two Master keys as if you only have one and you lose it, you have no way of programming any other keys and that will cost you a new ECU and in the words of my friendly Lexus dealer that will set you back four figures.
Anyway, here are the procedures.
Programming the transponder (immobiliser) first picture, door locks second picture. Before you start this part put yourself in the drivers seat, lock all the doors using the electric lock button, then unlock the drivers door using the manual switch. That's where you start at point 2.
Hope this helps someone.