The first odd items in what was Julia's room are the bell pull which has no apparent connection and the ventilator which, instead of being connected to the outside, is placed on the wall of the adjoining bedroom-
“They seem to have been of a most interesting character—dummy bell-ropes, and ventilators which do not ventilate."
Holmes has anticipated these two elements, and the third clue helps him reach his conclusion to the mystery. It is the positioning of the bed in the chamber which is the final clue-
“It was clamped to the floor. Did you ever see a bed fastened like that before?”