An end effector has one or more vortex chucks to support a wafer, and at least two detectors for detecting different portions of the wafer before the wafer is picked up. If one of the detectors detects a wafer and the other one does not, an alarm is generated to alert an operator that the wafer is possibly cross slotted in the wafer cassette. Each detector includes a light emitter and a light receiver. The light emitter emits a light beam at an angle to a surface defined by an ideally flat wafer when the wafer is supported by the end effector (the actual wafers do not have to be flat). The angle is not more than 45.degree., and is between 6.degree. and 12.degree. in some embodiments. Other features and embodiments are also provided.