readCelFile: Read raw intensities from CEL files
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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.

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

Benedikt Zacher zacher@lmb.uni-muenchen.de

readCelIntensities, xy2indices

##
# 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)