NormqPCR (version 1.18.0)

combineTechReps: Combines Technical Replicates

Description

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

Usage

combineTechReps(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

Value

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

Details

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

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))