Nearly half a billion years passed between the release of the now routinely observed Comic Microwave Backrgound and the formation of the first galaxies and black holes which reionized the ubiquitous hydrogen. This Epoch of Reionization (EoR) is the next major unexplored cosmological milestone. At the current time the space between galaxies is almost completely ionized, therefor we know that the universe must have undergone a global phase transition. The nature of the ionizing sources, whether young galaxies or accreting massive black holes is unknown. Neither do we know when this reionization occured or how long it took. Models suggest that we can detect fluctuations in the 21cm hydrogen emission line as ionization proceeds and high contrast ionized holes are carved in the neutral hydrogen. Detecting these fluctuations is one of the few direct probes of the reionization process but is a difficult task requiring a new generation of low frequency radio telescopes. Motivated by the breadth of unknowns, the Precision Array for Probing the Epoch of Reionization (PAPER) has been slowly building in complexity while folding the results of observations back into improving the design and operation of the telescope. As part of this process, this thesis analyzes early observations to explore three major areas of concern in detecting EoR: contamination by foreground sources, calibration stability and limiting sensitivity. Catalogs produced from this early data show good agreement with previous measurements. We conclude that the calibration is stable and sensitivity floors are close to the expected theoretical levels.