deltaCt: Perform normalization with a given housekeeping gene

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

Description

Normalise qPCR eset using a given housekeeping gene as control, then perform differential expression analysis using the delta delta Ct method

Usage

deltaCt(qPCRBatch, ...)
## S4 method for signature 'qPCRBatch'
deltaCt(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
deltaCq(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")

Arguments

qPCRBatch	qPCR-specific expression set, containing qPCR data.
...	Extra arguments, detailed below
hkgs	String containing the name of the name of the housekeeping gene which will be used to normalise the rest of the genes.
combineHkgs	Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the geometric mean. Housekeepers can be found using geNorm or NormFinder algorithms.
calc	use arithmetic or geometric mean.

Details

Takes expression set of qPCR values and normalises them using a housekeeping gene. Returns a qPCRBatch with exprs set of the same dimensions but with the given hkg value subtracted.

Value

qPCRBatch with exprs set of the same dimensions but with the given hkg value subtracted.

Author(s)

James Perkins [e-mail]

References

Kenneth Livak, Thomase Schmittgen (2001). Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2^DDCt Method. Methods 25, 402-408, 2001 http://www.ncbi.nlm.nih.gov/pubmed/11846609

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.

See Also

selectHKs, deltaDeltaCq

Examples

  path <- system.file("exData", package = "NormqPCR")
  taqman.example <- file.path(path, "example.txt")
  qPCRBatch.taqman <- read.taqman(taqman.example)
  hkgs<-"Actb-Rn00667869_m1"
  qPCRBatch.norm <- deltaCq(qPCRBatch =  qPCRBatch.taqman, hkgs = hkgs, calc="arith")
  head(exprs(qPCRBatch.norm))

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