selectHKgenes: Selection of reference/housekeeping genes

In SLqPCR: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH

Description

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

Usage

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) [e-mail]

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

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

Example output

###############################################################
Step  1 :
gene expression stability values M:
    HPRT1     YWHAZ    RPL13A       UBC      GAPD      SDHA       TBP      HMBS 
0.5160313 0.5314564 0.5335963 0.5700961 0.6064919 0.6201470 0.6397969 0.7206013 
      B2M      ACTB 
0.7747634 0.8498739 
average expression stability M:	 0.6362855 
gene with lowest stability (largest M value):	 ACTB 
Pairwise variation, ( 9 / 10 ):	 0.07646901 
###############################################################
Step  2 :
gene expression stability values M:
    HPRT1    RPL13A     YWHAZ       UBC      GAPD      SDHA       TBP      HMBS 
0.4705664 0.5141375 0.5271169 0.5554718 0.5575295 0.5738460 0.6042110 0.6759176 
      B2M 
0.7671985 
average expression stability M:	 0.5828883 
gene with lowest stability (largest M value):	 B2M 
Pairwise variation, ( 8 / 9 ):	 0.07765343 
###############################################################
Step  3 :
gene expression stability values M:
    HPRT1    RPL13A      SDHA     YWHAZ       UBC      GAPD       TBP      HMBS 
0.4391222 0.4733732 0.5243665 0.5253471 0.5403137 0.5560120 0.5622094 0.6210820 
average expression stability M:	 0.5302283 
gene with lowest stability (largest M value):	 HMBS 
Pairwise variation, ( 7 / 8 ):	 0.067112 
###############################################################
Step  4 :
gene expression stability values M:
    HPRT1    RPL13A     YWHAZ       UBC      SDHA      GAPD       TBP 
0.4389069 0.4696398 0.4879728 0.5043292 0.5178634 0.5245346 0.5563591 
average expression stability M:	 0.4999437 
gene with lowest stability (largest M value):	 TBP 
Pairwise variation, ( 6 / 7 ):	 0.06813202 
###############################################################
Step  5 :
gene expression stability values M:
    HPRT1    RPL13A       UBC     YWHAZ      GAPD      SDHA 
0.4292808 0.4447874 0.4594181 0.4728920 0.5012107 0.5566762 
average expression stability M:	 0.4773775 
gene with lowest stability (largest M value):	 SDHA 
Pairwise variation, ( 5 / 6 ):	 0.08061944 
###############################################################
Step  6 :
gene expression stability values M:
      UBC    RPL13A     HPRT1     YWHAZ      GAPD 
0.4195958 0.4204997 0.4219179 0.4424631 0.4841646 
average expression stability M:	 0.4377282 
gene with lowest stability (largest M value):	 GAPD 
Pairwise variation, ( 4 / 5 ):	 0.08416531 
###############################################################
Step  7 :
gene expression stability values M:
   RPL13A       UBC     YWHAZ     HPRT1 
0.3699163 0.3978736 0.4173706 0.4419220 
average expression stability M:	 0.4067706 
gene with lowest stability (largest M value):	 HPRT1 
Pairwise variation, ( 3 / 4 ):	 0.09767827 
###############################################################
Step  8 :
gene expression stability values M:
      UBC    RPL13A     YWHAZ 
0.3559286 0.3761358 0.3827933 
average expression stability M:	 0.3716192 
gene with lowest stability (largest M value):	 YWHAZ 
Pairwise variation, ( 2 / 3 ):	 0.113745 
###############################################################
Step  9 :
gene expression stability values M:
   RPL13A       UBC 
0.3492712 0.3492712 
average expression stability M:	 0.3492712 

SLqPCR documentation built on Nov. 8, 2020, 5:12 p.m.