selectHKgenes {SLqPCR} | R Documentation |
This function can be used to determine a set of reference/housekeeping (HK) genes for gene expression experiments.
selectHKgenes(relData, method = "Vandesompele", minNrHK = 2, geneSymbol, trace = TRUE, na.rm = FALSE)
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. |
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.
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 |
Dr. Matthias Kohl (SIRS-Lab GmbH) kohl@sirs-lab.com
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/
data(vandesompele) res.BM <- selectHKgenes(vandesompele[1:9,], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = TRUE, na.rm = TRUE)