getImage.AffymetrixCelFile {aroma.affymetrix}R Documentation

Creates an RGB Image object from a CEL file

Description

Creates an RGB Image object from a CEL file.

Usage

## S3 method for class 'AffymetrixCelFile':
getImage(this, other=NULL, transforms=list(sqrt), xrange=c(0, Inf), yrange=xrange, zrange=c(0, sqrt(2^16)), field=c("intensities", "stdvs", "pixels"), zoom=1, ..., readRectFcn=NULL, verbose=FALSE)

Arguments

other An optional AffymetrixCelFile of the same chip type, that is used for calculating the ratio (non-logged). Note, to get the log-ratios, the log() function has to be specified as the first transform in the list of transformations.
xrange, yrange vectors of length two specifying the (x0,x1) and (y0,y1) regions to be extracted. If NULL, the complete regions is used.
field One of the CEL file fields, i.e. "intensities", stdvs, or pixels.
zoom A numeric scale factor in (0,+Inf) for resizing the imaging. If 1, no resizing is done.
palette An optional vector of color code.
... Additional arguments passed to *readRawDataRectangle() and more function.
readRectFcn A function taking arguments 'xrange' and 'yrange', or NULL for the default read function.
verbose A logical or a Verbose object.

Value

Returns an Image object. If palette==NULL, the color code is Grayscale, otherwise TrueColor.

Author(s)

Ken Simpson (ksimpson[at]wehi.edu.au).

See Also

Image. For more information see AffymetrixCelFile.


[Package aroma.affymetrix version 1.2.0 Index]