Instrument setup system for a fluorescence analyzer

A method for determining compensation in an instrument for analyzing a multiplicity of fluorescent dyes using a multiplicity of photodetectors, each having an adjustable gain, wherein the instrument comprises a stored representation of the pairwise functional relationships between measured fluorescence and photodetector gain for each of the photodectors and for each of the fluorescent dyes;

• wherein the method comprises:
• a) selecting an initial set of photodetector gain settings;
• and
• b) calculating compensation for said initial set of photodetector gain settings using said functional relationships.

A method for determining compensation in an instrument for analyzing a multiplicity of fluorescent dyes, wherein said instrument comprises a multiplicity of photodetectors, each having an adjustable gain, said method comprising:

• a) determining and storing a representation of pairwise functional relationships between measured fluorescence and photodetector gain for each of said photodectors and for each of the fluorescent dyes;
• b) selecting an initial set of photodetector signal amplification settings;
• and
• c) calculating compensation for the initial set of photodetector signal amplification settings using said functional relationships.

A method, in an instrument for analyzing a multiplicity of fluorescent dyes using a multiplicity of photodetectors, each having an adjustable gain, wherein for each of said photodetectors, one of said fluorescent dyes is a primary dye, and wherein said instrument comprises an initial compensation matrix, of determining an adjusted compensation matrix from said initial compensation matrix following an adjustment of a photodetector gain, wherein said adjustment of a photodetector gain results in a change in fluorescence measured from a dye-containing sample from a first fluorescence level to a second fluorescence level, said method comprising the steps of:

• a) defining a brightness ratio, r, as the ratio of said second fluorescence level to said first fluorescence level;
• b) multiplying a row of the inverse of said initial compensation matrix corresponding to said adjusted photodetector by r to obtain an adjusted spillover matrix;
• c) multiplying a column of said adjusted spillover matrix corresponding to the primary dye for the adjusted photodetector by 1/r to obtain a normalized adjusted spillover matrix;
• d) inverting said normalized adjusted spillover matrix to obtain an adjusted compensation matrix.

A method, in an instrument for analyzing a multiplicity of fluorescent dyes using a multiplicity of photodetectors, each having an adjustable gain, of determining an adjusted quantitative result from an initial quantitative result following an adjustment of a photodetector gain from an initial photodetector gain to an adjusted photodetector gain, wherein said adjustment of a photodetector gain results in a change in fluorescence measured from a dye-containing sample from a first fluorescence level to a second fluorescence level, wherein said instrument comprises a stored functional relationship between quantitative result and fluorescence level, and said quantitative result is proportional to said fluorescence level, determined using said initial photodetector gain, said method comprising the steps of:

• a) defining a brightness ratio, r, as the ratio of said second fluorescence level to said first fluorescence level;
• b) measuring a fluorescence of a sample using said adjusted photodetector gain;
• c) determining an initial quantitative result said fluorescence of said sample using said functional relationship;
• d) multiplying said initial quantitative result by 1/r to obtain said adjusted quantitative result.