combineTechRepsSD: Combines Technical Replicates
In jimrperkins/NormqPCR: Functions for normalisation of RT-qPCR data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

combineTechRepsWithSD(qPCRBatch, ...)

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

`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

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.

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.

Matthias Kohl Matthias.Kohl@stamats.de

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.

combineTechReps

  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)