getImage.AffymetrixCelFile: Creates an RGB Image object from a CEL file

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

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.
...	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 as defined by the EBImage package. If palette==NULL, the color code is Grayscale, otherwise TrueColor.

Author(s)

Ken Simpson, Henrik Bengtsson

See Also

For more information see AffymetrixCelFile.

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