combineTechRepsWithSD {NormqPCR}R Documentation

Combines Technical Replicates

Description

Takes expression set of qPCR values containing technical replicates and combines them. In addition the appropriate standard deviation (SD) is computed.

Usage

combineTechRepsWithSD(qPCRBatch, ...)

## S4 method for signature 'qPCRBatch'
combineTechRepsWithSD(qPCRBatch, calc="arith") 

Arguments

qPCRBatch

Expression set containing qPCR data, read in by a ReadqPCR function and containing technical reps, denoted by _TechRep.n suffix.

...

Extra arguments, detailed below

calc

use median, arithmetic or geometric mean for combining the values

Details

Takes exprs of qPCR values containing technical replicates and combines them using a specified centrality measure.

The arithmetic mean (calc="arith") is combined with the classical standard deviation. In case of the geometric mean (calc="geom") the classical standard deviation of the log-values is exponentiated. The median (calc="median") is calculated in connection with the MAD.

Value

qPCRBatch with same number of samples, but with less features, since all technical replicates are replaced with a single value of their means. In addition the slot assayData includes a matrix with SD values which can be accessed via se.exprs.

Author(s)

Matthias Kohl Matthias.Kohl@stamats.de

References

Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.

See Also

combineTechReps

Examples

  path <- system.file("exData", package = "NormqPCR")
  qPCR.example.techReps <- file.path(path, "qPCR.techReps.txt")
  qPCRBatch.qPCR.techReps <- read.qPCR(qPCR.example.techReps)
  rownames(exprs(qPCRBatch.qPCR.techReps))
  combinedTechReps <- combineTechRepsWithSD(qPCRBatch.qPCR.techReps)
  rownames(exprs(combinedTechReps))
  exprs(combinedTechReps)
  se.exprs(combinedTechReps)

[Package NormqPCR version 1.36.0 Index]