getMOR.MAData: Gets the Measure of Reproducibility
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Value Author(s) References See Also Examples

Calculates the Measure of Reproducibility (MOR) [1], which is by default the (scalar) mean value of all genewise robust variability measures given by getGeneVariability(), either the standard deviation or the median absolute deviation (MAD). Any quantile(s) of these can be returned by setting argument probs.

1 2	## S3 method for class 'MAData' getMOR(this, robust=TRUE, probs=NULL, force=FALSE, slides=NULL, ...)

`robust`	If `TRUE` the median absolute deviation (MAD) will be used for calculating the genewise residuals, otherwise the sample standard deviation will be used.
`probs`	The quantiles of the genewise variabilities returned. If `-0.5` (or `NULL`) the mean is returned.
`force`	If `FALSE` and if cached gene variability values exists they will be used, otherwise the gene variability will be (re-)calculated.
`slides`	The slides which should be included in the calculations. If `NULL`, all slides are included.

Returns a vector of the quantiles of the genewise variabilities asked for. By default the mean value of all genewise variabilities (MOR) is returned.

Henrik Bengtsson (http://www.braju.com/R/)

[1] Henrik Bengtsson, Plate Effects in cDNA microarray data, Matemathical Statistics, Centre for Matematical Sciences, Lund University, Sweden. Manuscript, 2002.

*getVariability() For more information see MAData.

  SMA$loadData("mouse.data")
  layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
  raw <- RawData(mouse.data, layout=layout)
  ma <- getSignal(raw, bgSubtract=TRUE)
  ma.norm <- clone(ma)
  normalizeWithinSlide(ma.norm, method="s")
  normalizeAcrossSlides(ma.norm)
  mor <- getMOR(ma)
  mor.norm <- getMOR(ma.norm)

  cat("MOR for non-normalized data:", mor, "\n")
  cat("MOR for normalized data:", mor.norm, "\n")