selectHKgenes: Selection of reference/housekeeping genes

Description Usage Arguments Details Value Author(s) References Examples

View source: R/selectHKgenes.R

Description

This function can be used to determine a set of reference/housekeeping (HK) genes for gene expression experiments.

Usage

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selectHKgenes(relData, method = "Vandesompele", minNrHK = 2, geneSymbol, 
	      trace = TRUE, na.rm = FALSE)

Arguments

relData

matrix or data.frame containing relative expression values

method

method to compute most stable genes

minNrHK

minimum number of HK genes that should be considered

geneSymbol

gene symbols

trace

logical, print additional information

na.rm

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

Details

This function can be used to determine a set of reference/housekeeping (HK) genes for gene expression experiments. The default method "Vandesompele" was proposed by Vandesompele et al. (2002).

Currently, only the method by Vandesompele et al. (2002) is implemented.

Vandesompele et al. (2002) propose a cut-off value of 0.15 for the pairwise variation. Below this value the inclusion of an additional housekeeping gene is not required.

Value

If method = "Vandesompele" a list with the following components is returnd

ranking

ranking of genes from best to worst where the two most stable genes cannot be ranked

variation

pairwise variation during stepwise selection

meanM

average expression stability M

Author(s)

Dr. Matthias Kohl (SIRS-Lab GmbH) [email protected]

References

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/

Examples

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data(vandesompele)
res.BM <- selectHKgenes(vandesompele[1:9,], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = TRUE, na.rm = TRUE)

Bioconductor-mirror/SLqPCR documentation built on June 1, 2017, 2:08 a.m.