ECL`

AnalyzeQuantificationCycle

AnalyzeQuantificationCycle[Protocol]⟹Object

calculates the quantification cycle of each applicable amplification curve in the data linked to the provided quantitative polymerase chain reaction (qPCR) Protocol.

AnalyzeQuantificationCycle[Data]⟹Object

calculates the quantification cycle of each applicable amplification curve in the provided quantitative polymerase chain reaction (qPCR) Data.

Details

The quantification cycle is defined by default as the cycle at which the normalized and baseline-subtracted amplification curve crosses the fluorescence signal threshold set for that amplification target. If Method->Threshold, the amplification targets are defined by the unique sets of ForwardPrimer, ReversePrimer, and Probe (if applicable), and the quantification cycle for each amplification curve is determined via interpolation.
The quantification cycle is defined alternatively as the inflection point of the normalized and baseline-subtracted amplification curve. If Method->InflectionPoint, the quantification cycle is determined by fitting a logistic curve of the form a+b/(1+Exp[c*(x-InflectionPoint)]) to each amplification curve.

Input

Output

Method Options

Examples

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Basic Examples (3)

Given a qPCR data object, creates analysis object(s) for the data object:

Given a qPCR protocol object, creates analysis object(s) for each linked qPCR data object:

Given multiple qPCR data objects, creates analysis object(s) for each data object:

Options (8)

BaselineDomain (1)

BaselineDomain is automatically set to {'the larger of 3 Cycles and the first cycle of Domain', 15 Cycle}:

Domain (1)

Domain is automatically set to the first and last cycle from qPCR data:

ForwardPrimer (1)

ForwardPrimer is automatically set to unique forward primers from qPCR data if Method is set to Threshold:

Method (1)

Method can be specified:

Probe (1)

Probe is automatically set to unique probes from qPCR data if Method is set to Threshold:

ReversePrimer (1)

ReversePrimer is automatically set to unique reverse primers from qPCR data if Method is set to Threshold:

SmoothingRadius (1)

SmoothingRadius is automatically set to 2 cycles if Method is set to InflectionPoint:

Threshold (1)

Threshold is automatically set to 10 standard deviations above the mean fluorescence value in BaselineDomain if Method is set to Threshold:

Messages (14)

ForwardPrimerMissingFromqPCRData (1)

If ForwardPrimer is specified, the primer sample(s) must exist in the qPCR data inputs:

InflectionPointMethodTargetSpecified (1)

If Method->InflectionPoint, ForwardPrimer, ReversePrimer, and Probe must be Null:

InvalidBaselineDomainRange (1)

If BaselineDomain is specified, Baseline End Cycle must be greater than Baseline Start Cycle and less than or equal to either Analysis End Cycle or the minimum end cycle among all the amplification curves for analysis, and Baseline Start Cycle must be greater than or equal to Analysis Start Cycle:

InvalidDomainRange (1)

If Domain is specified, Analysis End Cycle must be greater than Analysis Start Cycle and less than or equal to the minimum end cycle among all the amplification curves for analysis:

InvalidThresholdLength (1)

If Threshold is specified, it must be either a singleton or a list matching the number of unique targets in the qPCR data:

MethodMismatch (1)

If Method->Threshold, SmoothingRadius cannot be specified and Threshold cannot be Null; if Method->InflectionPoint, SmoothingRadius cannot be Null and Threshold cannot be specified:

PrimerPairMismatch (1)

ForwardPrimer and ReversePrimer must both be either specified or Null:

PrimersProbeMismatch (1)

If ForwardPrimer and ReversePrimer are specified, Probe must be either specified or Null; if ForwardPrimer and ReversePrimer are Null, Probe must also be Null: