A method of DNA amplification comprising: - providing a plate including a plurality of wells; - providing a first mastermix including a suspension of ingredients, comprising samples of DNA, selected DNA primer strands, DNA elements, and enzymes, wherein said first mastermix emits a first spectrum in at least a first well of the plate, the first mastermix including a passive fluorescence dye that is a free, non-specific fluorescence dye which is not coupled to a sequence-specific probe; - providing a second mastermix including a suspension of ingredients, comprising samples of DNA, selected DNA primer strands, DNA elements, and enzymes, wherein said second mastermix does not emit the first spectrum in at least a second well of the plate, the second mastermix including an active fluorescence dye that is initially coupled to a sequence-specific probe to which a quencher is coupled that suppresses fluorescence of the active fluorescence dye; wherein the second mastermix is not provided in the same well as the first mastermix; wherein the active fluorescence dye is changed by decoupling it from the sequence-specific probe to emit the same measurable spectrum as the passive fluorescence dye; wherein the first mastermix is devoid of the active fluorescence dye coupled to the sequence-specific probe that includes the quencher and the second mastermix is devoid of the passive fluorescence dye that is not coupled to a sequence specific probe; wherein one of the dyes is used both in a passive manner to normalize the data, and in an active manner to detect DNA regions of interest; - performing a polymerase chain reaction in each of the first and second wells; - measuring an intensity of the passive and active fluorescence dyes for each cycle of the polymerase chain reaction; wherein the intensity of the active fluorescence dye indicates the amount of regions of interest in the samples of DNA in the mastermix; - storing data regarding the measured intensity of the passive and active fluorescence dyes for all cycles of the polymerase chain reaction; - extracting well-wise information from the data for the second well containing the active fluorescence dye, wherein well-wise information is information about the reaction in the specific well under consideration and accounts for the mastermix conditions in a well on different portions of the plate; - determining a slope, level and magnitude of noise for the background region of the amplification signal data for the second well by means of linear regression; and - extracting plate-wise information from the data for each well containing the passive fluorescence dye, wherein the data from all of the passive dye wells are combined, and wherein plate-wise information is information about the entire PCR, the plate, and the instrument, including non-optimal characteristics or non-PCR-related imperfection data and removing non-PCR-related imperfection data using signal intensity of the dyes for signal normalization based on the well-wise information from the active fluorescence dye and plate-wise information form the passive fluorescence dye. - providing a plate including a plurality of wells; - providing a first mastermix including a suspension of ingredients, comprising samples of DNA, selected DNA primer strands, DNA elements, and enzymes, wherein said first mastermix emits a first spectrum in at least a first well of the plate, the first mastermix including a passive fluorescence dye that is a free, non-specific fluorescence dye which is not coupled to a sequence-specific probe; - providing a second mastermix including a suspension of ingredients, comprising samples of DNA, selected DNA primer strands, DNA elements, and enzymes, wherein said second mastermix does not emit the first spectrum in at least a second well of the plate, the second mastermix including an active fluorescence dye that is initially coupled to a sequence-specific probe to which a quencher is coupled that suppresses fluorescence of the active fluorescence dye; - performing a polymerase chain reaction in each of the first and second wells; - measuring an intensity of the passive and active fluorescence dyes for each cycle of the polymerase chain reaction; wherein the intensity of the active fluorescence dye indicates the amount of regions of interest in the samples of DNA in the mastermix; - storing data regarding the measured intensity of the passive and active fluorescence dyes for all cycles of the polymerase chain reaction; - extracting well-wise information from the data for the second well containing the active fluorescence dye, wherein well-wise information is information about the reaction in the specific well under consideration and accounts for the mastermix conditions in a well on different portions of the plate; - determining a slope, level and magnitude of noise for the background region of the amplification signal data for the second well by means of linear regression; and - extracting plate-wise information from the data for each well containing the passive fluorescence dye,