getAverageFile.AffymetrixCelSet: Calculates the mean and the standard deviation of the cell...

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set

Description

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
getAverageFile(this, name=NULL, prefix="average", indices="remaining",
  field=c("intensities", "stdvs"), mean=c("median", "mean"), sd=c("mad", "sd"),
  na.rm=TRUE, g=NULL, h=NULL, ..., cellsPerChunk=moreCells * 10^7/length(this),
  moreCells=1, force=FALSE, verbose=FALSE)

Arguments

name	The label of the calculated parameters. If NULL, a default name format <prefix>-<mean>-<sd> is used.
indices	An integer vector specifying which cells to consider. If "remaining", only parameters for cells that have not been are calculated. If NULL, all cells are used.
mean	A character of a function specifying the function used to calculate the average.
sd	A character of a function specifying the function used to calculate the standard deviation.
na.rm	If TRUE, NAs are excluded before, otherwise not.
...	Not used.
cellsPerChunk	A integer specifying the total number of cells (across arrays) read into memory per chunk.
moreCells	A double scalar indicating if more or less cells should be used per chunk.
force	If TRUE, parameters for cells already calculated are recalculated, otherwise not.
verbose	If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

Details

The parameter estimates are stored as a CEL file of the same class as the data files in the set. The CEL file is named <name>.cel and placed in the directory of the set. Currently there is no specific data class for this file, but the average cell signals are stored as "intensities", the standard deviation of the cell signals as "stddevs", and the number of data points used for each estimate is stored as "pixels".

Value

Returns an AffymetrixCelSet of the same class as the CEL set averaged.

Author(s)

Henrik Bengtsson, Ken Simpson

See Also

For more information see AffymetrixCelSet.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.