combineTechRepsWithSD {NormqPCR} | R Documentation |
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 |
... |
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.
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)