getMOR2003a.MAData: Gets the Intensity Adjusted Measure of Reproducibility
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Value Author(s) See Also Examples

Calculates the Adjusted Measure of Reproducibility (MOR2003a), 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), weighted by the inverse of the estimated standard deviation of the log-ratios at the given log-intensities. Any quantile(s) of these can be returned by setting argument probs.

1 2	## S3 method for class 'MAData' getMOR2003a(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 (MOR2003a) is returned.

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

*getAdjustedSpotVariability() *getMOR() *getSpotVariability() For more information see MAData.

  SMA$loadData("mouse.data")
  # Keep only slides of treatment 1
  mouse.data <- lapply(mouse.data, FUN=function(x) x[,4:6])
  layout <- Layout$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 <- getMOR2003a(ma)
  mor.norm <- getMOR2003a(ma.norm)

  cat("MOR2003a for non-normalized data:", mor, "\n")
  cat("MOR2003a for normalized data:", mor.norm, "\n")