We analyze the density field of galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) included in the SDSS Data Release Nine (DR9). DR9 includes spectroscopic redshifts for over 400,000 galaxies spread over a footprint of 3,275 deg^2. We identify, characterize, and mitigate the impact of sources of systematic uncertainty on large-scale clustering measurements, both for angular moments of the redshift-space correlation function and the spherically averaged power spectrum, P(k), in order to ensure that robust cosmological constraints will be obtained from these data. A correlation between the projected density of stars and the higher redshift (0.43 < z < 0.7) galaxy sample (the `CMASS sample) due to imaging systematics imparts a systematic error that is larger than the statistical error of the clustering measurements at scales s > 120h^-1Mpc or k < 0.01hMpc^-1. We find that these errors can be ameliorated by weighting galaxies based on their surface brightness and the local stellar density. We use mock galaxy catalogs that simulate the CMASS selection function to determine that randomly selecting galaxy redshifts in order to simulate the radial selection function of a random sample imparts the least systematic error on correlation function measurements and that this systematic error is negligible for the spherically averaged correlation function. The methods we recommend for the calculation of clustering measurements using the CMASS sample are adopted in companion papers that locate the position of the baryon acoustic oscillation feature (Anderson et al. 2012), constrain cosmological models using the full shape of the correlation function (Sanchez et al. 2012), and measure the rate of structure growth (Reid et al. 2012). (abridged)
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