combineTechReps: Combines Technical Replicates

In 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))

Example output

Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ReadqPCR
Loading required package: affy
Loading required package: qpcR
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: Matrix
Warning messages:
1: In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl_init' failed, running with rgl.useNULL = TRUE 
4: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Warning message:
In read.qPCR(qPCR.example.techReps) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.

 [1] "gene_aj_TechReps.1" "gene_aj_TechReps.2" "gene_al_TechReps.1"
 [4] "gene_al_TechReps.2" "gene_ax_TechReps.1" "gene_ax_TechReps.2"
 [7] "gene_bo_TechReps.1" "gene_bo_TechReps.2" "gene_cp_TechReps.1"
[10] "gene_cp_TechReps.2" "gene_dx_TechReps.1" "gene_dx_TechReps.2"
[13] "gene_ei_TechReps.1" "gene_ei_TechReps.2" "gene_jy_TechReps.1"
[16] "gene_jy_TechReps.2"
[1] "gene_aj" "gene_al" "gene_ax" "gene_bo" "gene_cp" "gene_dx" "gene_ei"
[8] "gene_jy"

NormqPCR documentation built on Nov. 8, 2020, 6:37 p.m.