(a) providing a first reaction mixture comprising the sample and a first plurality of hybridization probes,

wherein a hybridization probe of the first plurality of hybridization probes is specific for an analyte of the at least three polynucleotide analytes, wherein the first plurality of hybridization probes comprises hybridization probes specific for at least two of the at least three polynucleotide analytes, wherein the hybridization probes specific for the at least two of the at least three polynucleotide analytes comprise a first fluorophore that is identical for the first plurality of hybridization probes, wherein a first hybridization probe generates a first signal intensity in an amplification reaction, wherein a second hybridization probe generates a second signal intensity in the amplification reaction different from the first signal intensity, wherein a signal intensity of the first reaction mixture in the amplification reaction corresponds to a combination of presence or absence of the at least three polynucleotide analytes, wherein at least one combination of analytes produces a same signal intensity as a second combination of analytes, thereby producing an ambiguity between at least two combinations of analytes;

(b) providing a second reaction mixture comprising the sample and a second plurality of hybridization probes,

wherein a hybridization probe of the second plurality of hybridization probes is specific for an analyte of the at least three polynucleotide analytes, wherein the second plurality of hybridization probes comprises hybridization probes specific for at least two of the at least three polynucleotide analytes, wherein the hybridization probes specific for the at least two of the at least three polynucleotide analytes comprise a second fluorophore that is identical for the second plurality of hybridization probes, wherein a third hybridization probe generates a third signal intensity in an amplification reaction, wherein a fourth hybridization probe generates a fourth signal intensity in the amplification reaction different from the third signal intensity, wherein a signal intensity of the second reaction mixture in the amplification reaction corresponds to a combination of presence or absence of the at least three polynucleotide analytes;

(c) generating the signal intensity of the first reaction mixture using a first amplification reaction and generating the signal intensity of the second reaction mixture using a second amplification reaction; and

(d) processing the signal intensity of the first reaction mixture and the signal intensity of the second reaction mixture to generate a combined output, wherein the combined output unambiguously identifies a given combination of presence or absence of the at least three polynucleotide analytes in the sample, thereby resolving the ambiguity.