readCelFile {Starr} | R Documentation

## 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

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### 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)

[Package Starr version 1.38.0 Index]