ddCtExpression-methods {ddCt} | R Documentation

## Apply the ddCt algorithm for a given data set

### 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:r.biczok@dkfz.de

### 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

[Package ddCt version 1.42.0 Index]