Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set.
# S3 method for 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)Returns an AffymetrixCelSet of the same class as the CEL set
averaged.
The label of the calculated parameters.
If NULL, a default name format <prefix>-<mean>-<sd> is used.
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.
A character of a function specifying the function used
to calculate the average.
A character of a function specifying the function used
to calculate the standard deviation.
Not used.
A integer specifying the total number of cells
(across arrays) read into memory per chunk.
A double scalar indicating if more or less cells
should be used per chunk.
If TRUE, parameters for cells already calculated are
recalculated, otherwise not.
If TRUE, progress details are printed, otherwise not.
May also be a Verbose object.
Henrik Bengtsson, Ken Simpson
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".
For more information see AffymetrixCelSet.