combineTechReps: Combines Technical Replicates

In jimrperkins/NormqPCR: Functions for normalisation of RT-qPCR data

Description

Takes expression set of qPCR values containing technical replicates and combines them.

Usage

combineTechReps(qPCRBatch, ...)

## S4 method for signature 'qPCRBatch'
combineTechReps(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.

Value

qPCRBatch with same number of samples, but with less features, since all technical replicates are replaced with a single value of their means.

Author(s)

James Perkins [e-mail]

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.

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 <- combineTechReps(qPCRBatch.qPCR.techReps)
  rownames(exprs(combinedTechReps))

jimrperkins/NormqPCR documentation built on March 6, 2020, 1:06 a.m.