stabMeasureRho: Gene expression stability value rho

In NormqPCR: Functions for normalisation of RT-qPCR data

Description

Computation of the gene expression stability value rho for real-time quantitativ RT-PCR data. For more details we refer to Andersen et al. (2004).

Usage

  stabMeasureRho(x,...)

  ## S4 method for signature 'x'
stabMeasureRho(x, group, log = TRUE, na.rm = TRUE, returnAll = FALSE)

Arguments

x	matrix containing real-time quantitative RT-PCR data, or qPCRBatch object
...	Extra arguments, detailed below
group	grouping factor, either a factor vector or a phenoData column called "Group"
log	logical: is data on log-scale
na.rm	a logical value indicating whether NA values should be stripped before the computation proceeds.
returnAll	logical, return additional information.

Details

The gene expression stability value rho is computed. For more details see Andersen et al. (2004).

Value

numeric vector with gene expression stability values

If returnAll == TRUE a list with the following components is returned

rho	stability measure rho of Andersen et al. (2004)
d	used by selectHKs
v	used by selectHKs

Author(s)

Matthias Kohl [e-mail]

References

Claus Lindbjerg Andersen, Jens Ledet Jensen and Torben Falck Orntoft (2004). Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. CANCER RESEARCH 64, 5245-5250, August 1, 2004. http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245

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.

See Also

selectHKs

Examples

  data(Colon)
  Class <- pData(Colon)[,"Classification"]
  res.Colon <- stabMeasureRho(Colon, group = Class, log = FALSE)
  sort(res.Colon) # cf. Table 3 in Andersen et al (2004)
  
  data(Bladder)
  Grade <- pData(Bladder)[,"Grade"]
  res.Bladder <- stabMeasureRho(Bladder, group = Grade, log = FALSE)
  sort(res.Bladder) # cf. Table 3 in Andersen et al (2004)

Example output

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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: affy
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 read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl_init' failed, running with rgl.useNULL = TRUE 
4: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Warning message:
In .local(x, ...) : Argument 'group' is transformed to a factor vector.
      UBC      GAPD      TPT1       UBB     TUBA6     RPS13      NACA      CFL1 
0.1821707 0.2146061 0.2202956 0.2471573 0.2700641 0.2813039 0.2862397 0.2870467 
     SUI1      ACTB      CLTC     RPS23  FLJ20030 
0.3139404 0.3235918 0.3692880 0.3784909 0.3935173 
Warning message:
In .local(x, ...) : Argument 'group' is transformed to a factor vector.
    HSPCB      TEGT     ATP5B       UBC     RPS23     RPS13      CFL1  FLJ20030 
0.1539598 0.1966556 0.1987227 0.2033477 0.2139626 0.2147852 0.2666129 0.2672918 
     TPT1       UBB     FLOT2      GAPD    S100A6      ACTB 
0.2691553 0.2826051 0.2960429 0.3408742 0.3453435 0.3497295 

NormqPCR documentation built on Nov. 8, 2020, 6:37 p.m.