ddCtExpression-class: ddCt Expression

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

Description

This class is a subclass of ExpressionSet and represents objects which are produced by the ddCt algorithm in the ddCtExpression method

Extends

Class ExpressionSet, directly. Class eSet, by class "ExpressionSet", distance 2. Class VersionedBiobase, by class "ExpressionSet", distance 3. Class Versioned, by class "ExpressionSet", distance 4.

Methods

Ct

signature(object = "ddCtExpression"): returns the Ct value of this ddCtExpressionobject

CtErr

signature(object = "ddCtExpression"): returns the error number of the Ct value of this ddCtExpressionobject

dCt

signature(object = "ddCtExpression"): returns the dCt value of this ddCtExpressionobject

dCtErr

signature(object = "ddCtExpression"): returns the error number of the dCt value of this ddCtExpressionobject

ddCt

signature(object = "ddCtExpression"):returns the ddCt value of this ddCtExpressionobject

ddCtErr

signature(object = "ddCtExpression"): returns the error number of the ddCt value of this ddCtExpressionobject

level

signature(object = "ddCtExpression"): returns the levels in this ddCtExpressionobject

levelErr

signature(object = "ddCtExpression"): returns the error number of the levens in this ddCtExpressionobject

numberCt

signature(object = "ddCtExpression"): returns the Ct number of this ddCtExpressionobject

numberNA

signature(object = "ddCtExpression"): returns the NA number of this ddCtExpressionobject

elist

signature(object = "ddCtExpression"): returns a data frame which represents this expression object

elistWrite

signature(object = "ddCtExpression", file = "character"): writes ddCtExpression object into a file

Author(s)

Rudolf Biczok mailto:[e-mail]

See Also

SDMFrame: reader for SDM files elist, elistWrite: utility functions for ddCtExpression objects ddCtExpression: the method which invokes the ddCt algorithm

Examples

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

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

## use getter methods
ddCt(result)
ddCtErr(result)

Example output

        Sample
Detector Sample1   Sample2
   Gene1       0 -3.029402
   Gene2       0  3.029402
   Gene3       0  1.702378
        Sample
Detector Sample1   Sample2
   Gene1       0 0.3743327
   Gene2       0 0.3743327
   Gene3       0 0.8661806

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