ddCtExpression-methods {ddCt} | R Documentation |
Apply the ddCt algorithm for a given data set
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 |
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. |
A an object of class
ddCtExpression
.
ddCtExpression(object, warningStream = "warning.output.txt", algorithm="ddCt" calibrationSample, housekeepingGenes, type="mean", sampleInformation=NULL, toZero=TRUE, efficiencies = NULL, efficiencies.error = NULL)
An object of InputFrame
,
constructed with the method InputFrame
Rudolf Biczok mailto:r.biczok@dkfz.de
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
InputFrame
: reader for SDM files
ddCtExpression
: representation for ddCt
calculated expressions
## 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