ddCt (version 1.28.0)

ddCtExpression-methods: 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

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

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