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The Epoch of Reionization (EoR) is an uncharted era in our Universe's historyduring which the birth of the first stars and galaxies led to the ionization ofneutral hydrogen in the intergalactic medium. There are many experimentsinvestigating the EoR by tracing the 21cm line of neutral hydrogen. Becausethis signal is very faint and difficult to isolate, it is crucial to developanalysis techniques that maximize sensitivity and suppress contaminants indata. It is also imperative to understand the trade-offs between differentanalysis methods and their effects on power spectrum estimates. Specifically,with a statistical power spectrum detection in HERA's foreseeable future, ithas become increasingly important to understand how certain analysis choicescan lead to the loss of the EoR signal. In this paper, we focus on signal lossassociated with power spectrum estimation. We describe the origin of this lossusing both toy models and data taken by the 64-element configuration of theDonald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER).In particular, we highlight how detailed investigations of signal loss have ledto a revised, higher 21cm power spectrum upper limit from PAPER-64.Additionally, we summarize errors associated with power spectrum errorestimation that were previously unaccounted for. We focus on a subset ofPAPER-64 data in this paper; revised power spectrum limits from the PAPERexperiment are presented in a forthcoming paper by Kolopanis et al. (in prep.)and supersede results from previously published PAPER analyses.

Characterizing Signal Loss in the 21 cm Reionization Power Spectrum: A Revised Study of PAPER-64