1. A method of estimating a number of nucleotide incorporations when sequencing a polynucleotide strand, comprising: flowing a series of nucleotide flows onto a reactor array comprising a plurality of chemFET sensors and 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, wherein the one or more copies of the polynucleotide strand are attached to a substrate particle; receiving output signals from the plurality of chemFET sensors of the reactor array, the output signals being generated in response to chemical reactions between the one or more copies of the polynucleotide strand and the series of nucleotide flows; determining a background signal for the loaded reaction confinement region using a model of an output signal from the loaded reaction confinement region, the model of the output signal from the loaded reaction confinement region being a linear combination of a function of a first signal component and a function of a second signal component, wherein determining the background signal comprises fitting the model to the received output signals based on at least a ratio parameter of the function of the second signal component, wherein: the second signal component is generated based on an output signal from an unloaded reaction confinement region of the reactor array, and the function of the second signal component comprises (i) a rate parameter that varies mathematically with a rate of change in an amount of hydrogen ions in the loaded reaction confinement region, and (ii) the ratio parameter, which ratio parameter varies mathematically with a ratio of a rate of change in the amount of hydrogen ions in the unloaded reaction confinement region relative to the rate of change in the amount of hydrogen ions in the loaded reaction confinement region; determining an incorporation signal from the loaded reaction confinement region using the model of the output signal from the loaded reaction confinement region, wherein determining the incorporation signal further comprises fitting the model to at least some of the received output signals based on one or more parameters of the function of the first signal component; and determining an estimate of a number of nucleotides incorporated into the polynucleotide strand using a method selection from (i) using a peak of the determined incorporation signal to estimate the number of nucleotides incorporated, and (ii) comparing the determined incorporation signal to a set of reference incorporation signal curves to estimate the number of nucleotides incorporated.