ddCt {prada}R Documentation

Apply the ddCt method for a given data set

Description

Apply the ddCt method for a given data set

Usage

ddCt(raw.table,calibrationSample,housekeepingGenes,type="mean",sampleInformation=NULL,toZero=FALSE,filename="warning.output.txt")

Arguments

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

Details

Please see vignette 'How to apply the ddCt method' in the ddCt package for details.

Value

A an object of class eSet. The assayData has the following components: exprs(the level), level.err, Ct, Ct.error, dCt, dCt.error, ddCt, ddCt.error, Difference, number_NA, number, Plate.

Author(s)

Markus Ruschhaupt mailto:m.ruschhaupt@dkfz.de

See Also

readSDM,eListWrite

Examples

##see vignette rtPCR.pdf

[Package prada version 1.8.0 Index]