1. A method of sequencing a polynucleotide strand, comprising: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array; receiving output signals from the reactor array; determining a background signal for the loaded reaction confinement region using a model of an output signal from the loaded reaction confinement region; determining an incorporation signal from the loaded reaction confinement region using the model of an output signal from the loaded reaction confinement region; and determining an estimate of a number of nucleotides incorporated into the polynucleotide strand.