read.celfile.probeintensity.matrices {affyio}R Documentation

Read PM or MM from CEL file into matrices

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 <bmb@bmbolstad.com>


[Package affyio version 1.4.1 Index]