ddCtExpression-methods: Apply the ddCt algorithm for a given data set

In ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

Description

Apply the ddCt algorithm for a given data set

Arguments

object	SDMFrame Data object which holds a data set containing columns with the following names: 'Ct','Sample','Detector','Platename'. The column 'Ct' must contain numeric values.
algorithm	character. Name of the calibration samples.
warningStream	character of length 1. The name of the file the warnings should be stored in.
calibrationSample	character. Name of the calibration samples.
housekeepingGenes	character. Name of the housekeeping genes.
type	character of length 1. 'mean' or 'median'- which method should be used for the aggregation of the repicates
sampleInformation	if specified it must be an object of class phenoData with a column named 'Sample'.
toZero	boolean - if there is only one replication should the error be treated as zero ? (only if 'type' is mean)
efficiencies	n.V.
efficiencies.error	n.V.

Value

A an object of class ddCtExpression.

usage

ddCtExpression(object, warningStream = "warning.output.txt", algorithm="ddCt" calibrationSample, housekeepingGenes, type="mean", sampleInformation=NULL, toZero=TRUE, efficiencies = NULL, efficiencies.error = NULL)

Methods

object = "InputFrame"

An object of InputFrame, constructed with the method InputFrame

Author(s)

Rudolf Biczok mailto:[e-mail]

References

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta -Delta C(T)) Method. KJ Livak and TD Schmittgen, Methods, Vol. 25, No. 4. (December 2001), pp. 402-408

See Also

InputFrame: reader for SDM files ddCtExpression: representation for ddCt calculated expressions

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt", package="ddCt"))

## call ddCtExpression method from class SDMFrame
## to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))
result

Example output

ddCtExpression (storageMode: list)
assayData: 3 features, 2 samples 
  element names: exprs, level.err, Ct, Ct.error, dCt, dCt.error, ddCt, ddCt.error, Difference, numberNA, number, Plate 
protocolData: none
phenoData
  sampleNames: Sample1 Sample2
  varLabels: Sample Calibrator
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  

ddCt documentation built on Nov. 8, 2020, 4:57 p.m.