1. A method for operating an array of sensors arranged in rows and columns, a row including a plurality of sensors, each sensor in the plurality including a chemically-sensitive field effect transistor (chemFET) having an output, each sensor being configured to use the chemFET to produce a signal on the output in response to a row select signal, and a plurality of column output circuits coupled to the outputs of a column of sensors in the array, the method comprising: providing a reference voltage to the plurality of column output circuits during a calibration operation; and using outputs of the plurality of column output circuits in response to the provided reference voltage to compensate for variances among the plurality of column output circuits, wherein a column output circuit in the plurality of column output circuits includes a column sample and hold capacitor, and using the column sample and hold capacitor to sample the signal from each sensor in the column of sensors in sequence, wherein each sensor in the plurality of sensors includes a chemical sample well, wherein the chemFET in each sensor in the plurality of sensors includes a floating gate and a passivation layer, and the signal on the output indicates an ion-concentration in an analyte solution coupled to the floating gate via the passivation layer.