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Depends on the thermometer. Im assuming by your question you are referring to a digital thermometer with a remote probe.
In that case, just the probe goes in the chamber.
If you are using a bulb or discrete thermometer, like a childrens model, then the whole thing goes in the chamber.
However, no matter which you use, place the sensing section of the the thermometer in a water weasel. Heres a link to explain this:
http://shilala.homestead.com/weasel.html
But dont buy one frome these guys. $12 is too much. Sorry.
Get one from
WalMart or the toy store for $1. Youll find them in the toy section next to the the liquid bubbles and stuff.
You can also make a good one from a ziplock baggie. Fill it partially with water and squeeze all the air out as you seal it. Then roll it into a ball, about the size of an egg, and wrap a rubber band around it.
The point of all this is to simulate an egg in the chamber, so you monitor the actual temp of the egg and not the air temp itself.
Air temps in small incubators can be widely variable, and are rarely close to the actual temperature of the egg.