Methods and apparatus for measuring analytes using large scale FET arrays

An apparatus comprising:

• a chemical-sensitive field effect transistor (chemFET) array formed in a semiconductor substrate, the chemFET array having an overlayed array of reaction chambers wherein each reaction chamber is in contact with or capacitively coupled to at least one chemFET, wherein the chemFETs each have a floating gate with zero or substantially zero trapped charge, so that chemFETs of the array have output levels without appreciable variation across the array;
• and,
• a flow cell member configured and arranged for receiving and exposing the array of reaction chambers to a fluid flow of reagents, the flow cell member being configured so that such reagents are delivered transversely over an open portion of each reaction chamber with uniform transit times across the array of reaction chambers, wherein the flow cell member has an inlet and an outlet positioned at opposite corners of the flow cell.