NormqPCR (version 1.18.0)

stabMeasureRho: Gene expression stability value rho

Description

Computation of the gene expression stability value rho for real-time quantitativ RT-PCR data. For more details we refer to Andersen et al. (2004).

Usage

stabMeasureRho(x,...)
  "stabMeasureRho"(x, group, log = TRUE, na.rm = TRUE, returnAll = FALSE)

Arguments

x

matrix containing real-time quantitative RT-PCR data, or qPCRBatch object

...

Extra arguments, detailed below

group

grouping factor, either a factor vector or a phenoData column called "Group"

log

logical: is data on log-scale

na.rm

a logical value indicating whether NA values should be stripped before the computation proceeds.

returnAll

logical, return additional information.

Value

numeric vector with gene expression stability valuesIf returnAll == TRUE a list with the following components is returned

rho

stability measure rho of Andersen et al. (2004)

d

used by selectHKs

v

used by selectHKs

Details

The gene expression stability value rho is computed. For more details see Andersen et al. (2004).

References

Claus Lindbjerg Andersen, Jens Ledet Jensen and Torben Falck Orntoft (2004). Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. CANCER RESEARCH 64, 5245-5250, August 1, 2004. http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245

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

Examples

  data(Colon)
  Class <- pData(Colon)[,"Classification"]
  res.Colon <- stabMeasureRho(Colon, group = Class, log = FALSE)
  sort(res.Colon) # cf. Table 3 in Andersen et al (2004)
  
  data(Bladder)
  Grade <- pData(Bladder)[,"Grade"]
  res.Bladder <- stabMeasureRho(Bladder, group = Grade, log = FALSE)
  sort(res.Bladder) # cf. Table 3 in Andersen et al (2004)