Starr (version 1.28.0)

readCelFile: Read raw intensities from CEL files

Description

Function to read the raw intensities of the perfect match probes (PM) of Affymetrix CEL files into an ExpressionSet. This function is used to read one-color data. For two-color data use the functions from the Ringo package.

Usage

readCelFile(bpmap, cel_files, names, type, experimentData=NULL, featureData=T, log.it=T, phenodata=NULL)

Arguments

bpmap

Either a list, created by the function readBpmap() from the affy package, or the path to the bpmap file.

cel_files

a character vector, specifying the path to the CEL files

names

a character vector, containing the names of the experiments

type

a character vector, containing the type of experiment, e.g. "IP" for an Immunoprecipitation, or "CONTROL" for a control or reference experiment was done

experimentData

This must be an object of type MIAME, which details information about e.g., the investigator or lab where the experiment was done, an overall title, and other notes

featureData

If TRUE, a featureData object is added to the ExpressionSet, containing information about the chromosome, position in the genome and sequence of the features

log.it

If TRUE, logged intesities are read

phenodata

data.frame, containing columns name, type, CEL.

Value

Returns raw intensity values in form of an ExpressionSet with additional information:

assayData

This object contains the measured probe intensities.

phenoData

contains further description of the experiments, such as names or type

featureData

containing information about the chromosome, position in the genome and sequence of the features

experimentData

details information about e.g., the investigator or lab where the experiment was done

See Also

readCelIntensities, xy2indices

Examples

##
# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
# 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
# names <- c("rpb3_1", "wt_1","rpb3_2")
# type <- c("IP", "CONTROL", "IP")
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)