stabMeasureM: Gene expression stability value M
In jimrperkins/NormqPCR: Functions for normalisation of RT-qPCR data

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

Computation of the gene expression stability value M for real-time quantitativ RT-PCR data. For more details we refer to Vandesompele et al. (2002).

1	stabMeasureM(x, log = TRUE, na.rm = TRUE)

`x`	matrix or data.frame containing real-time quantitative RT-PCR data
`log`	logical: is data on log-scale
`na.rm`	a logical value indicating whether `NA` values should be stripped before the computation proceeds.

The gene expression stability value M is defined as the average pairwise normalization factor; i.e., one needs to specify data from at least two genes. For more details see Vandesompele et al. (2002). Note this dispatches on a transposed expression matrix, not a qPCRBatch object since it is only called from within the selectHKs method.

numeric vector with gene expression stability values

Matthias Kohl Matthias.Kohl@stamats.de

Jo Vandesompele, Katleen De Preter, Filip Pattyn et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 2002. 3(7):research0034.1-0034.11. http://genomebiology.com/2002/3/7/research/0034/

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.

selectHKs

  data(geNorm)
  tissue <- as.factor(c(rep("BM", 9),  rep("FIB", 20), rep("LEU", 13),
                    rep("NB", 34), rep("POOL", 9)))
  res.BM <- selectHKs(geNorm.qPCRBatch[,tissue == "BM"], method = "geNorm", 
                    Symbols = featureNames(geNorm.qPCRBatch), minNrHK = 2, log = FALSE)