stabMeasureM: Gene expression stability value M
In 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)

Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ReadqPCR
Loading required package: qpcR
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase

Attaching package: ‘robustbase’

The following object is masked from ‘package:Biobase’:

    rowMedians

Loading required package: Matrix
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
###############################################################

Step 1:

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 stability M:	0.63628545246682

variable with lowest stability (largest M value):	ACTB

Pairwise variation, (9/10):	0.0764690052563778

###############################################################

Step 2:

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 stability M:	0.582888329316757

variable with lowest stability (largest M value):	B2M

Pairwise variation, (8/9):	0.0776534266912183

###############################################################

Step 3:

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 stability M:	0.530228279613623

variable with lowest stability (largest M value):	HMBS

Pairwise variation, (7/8):	0.0671119963410967

###############################################################

Step 4:

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 stability M:	0.499943693933222

variable with lowest stability (largest M value):	TBP

Pairwise variation, (6/7):	0.0681320232188603

###############################################################

Step 5:

stability values M:

    HPRT1    RPL13A       UBC     YWHAZ      GAPD      SDHA 
0.4292808 0.4447874 0.4594181 0.4728920 0.5012107 0.5566762 
average stability M:	0.477377523800525

variable with lowest stability (largest M value):	SDHA

Pairwise variation, (5/6):	0.0806194432580746

###############################################################

Step 6:

stability values M:

      UBC    RPL13A     HPRT1     YWHAZ      GAPD 
0.4195958 0.4204997 0.4219179 0.4424631 0.4841646 
average stability M:	0.437728198765878

variable with lowest stability (largest M value):	GAPD

Pairwise variation, (4/5):	0.0841653121631615

###############################################################

Step 7:

stability values M:

   RPL13A       UBC     YWHAZ     HPRT1 
0.3699163 0.3978736 0.4173706 0.4419220 
average stability M:	0.406770625156432

variable with lowest stability (largest M value):	HPRT1

Pairwise variation, (3/4):	0.097678269387021

###############################################################

Step 8:

stability values M:

      UBC    RPL13A     YWHAZ 
0.3559286 0.3761358 0.3827933 
average stability M:	0.371619241507029

variable with lowest stability (largest M value):	YWHAZ

Pairwise variation, (2/3):	0.113745049966055

###############################################################

Step 9:

stability values M:

   RPL13A       UBC 
0.3492712 0.3492712 
average stability M:	0.349271187472188