read.celfile.probeintensity.matrices: Read PM or MM from CEL file into matrices

In affyio: Tools for parsing Affymetrix data files

Description

This function reads PM, MM or both types of intensities into matrices. These matrices have all the probes for a probeset in adjacent rows

Usage

read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both"))

Arguments

filenames	a character vector of filenames
cdfInfo	a list with items giving PM and MM locations for desired probesets. In same structure as returned by make.cdf.package
rm.mask	a logical. Return these probes as NA if there are in the [MASK] section of the CEL file
rm.outliers	a logical. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file

.

rm.extra

a logical. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file

.

verbose	a logical. When true the parsing routine prints more information, typically useful for debugging.
which	a string specifing which probe type to return

Value

returns a list of matrix items. One matrix contains PM probe intensities, with probes in rows and arrays in columns

Author(s)

B. M. Bolstad <[e-mail]>

affyio documentation built on Nov. 8, 2020, 6:53 p.m.