preprocessingGE {PREDA} | R Documentation

## Wrapper function for gene expression data preprocessing for differential expression analysis with PREDA

### Description

Wrapper function for gene expression data preprocessing for differential expression analysis with PREDA

### Usage

    preprocessingGE(SampleInfoFile = NULL, CELfiles_dir = NULL,
    AffyBatchInput = NULL, custom_cdfname, arrayNameColumn = NULL,
    sampleNameColumn = NULL, classColumn,
    referenceGroupLabel, statisticType, optionalAnnotations = NULL,
    retain.chrs = NULL, reference_position_type = "median",
    testedTail = "both")

### Arguments

`SampleInfoFile` | Path to sample info file
`CELfiles_dir` | Path to directory containing raw CEL data files for Affymetrix arrays
`AffyBatchInput` | Alternatively input raw data can be provided as an AffyBatch object. In this case sample classes will be inferred from phenodata contained in AffyBatch object. In particular classColumn parameter will refer to the column in pData(AffyBatchInput) object.
`custom_cdfname` | Specify the cdf library to be used for data preprocessing
`arrayNameColumn` | Column of sampleinfo file containing the name of raw data (CEL) files
`sampleNameColumn` | Column of sampleinfo file containing the name to be used for samples labels
`classColumn` | Column of sampleinfo file containing the label of sample classes. If input raw data are provided as an AffyBatch object, this parameter refers intead to the column in pData(AffyBatchInput) object.
`referenceGroupLabel` | Specify which class label is used for the reference sample used in computing statistics for differential expression.
`statisticType` | Stastistic for differential expression that is computed on input data. Possible values are "tstatistic", "FC" (Fold Change), "FCmedian" (fold change computed on medians)
`optionalAnnotations` | Character vector to select additional annotations fields to be included into the GenomicAnnotations object.
`retain.chrs` | Numeric vector, containing the list of chromosomes selected for the output GenomicAnnotations object. E.g. set retain.chrs=1:22 to limit the GenomicAnnotations object to chromosomes from 1 to 22. This might be ueseful to limit GenomiAnnotations objects to autosomic chromosomes.
`reference_position_type` | Specify which genomic coordinate must be used as reference position for PREDA analysis. Possible values are "start", "end", "median", "strand.start" or "strand.end".
`testedTail` | Specify what tail of the distribution will be tested for significantly extreme values in PREDA analysis. Possible values are "both", "upper" or "lower".

### Details

Preprocess raw (CEL) files for Affymetrix gene expression arrays using user defined CDF libraries and RMA normalization. Then statistics for differential expression are computed. Then annotations are retrieved from the corresponding annotation library.

Please note this function is a user-friendly preprocessing function for Affy gene expression microarrays. Step by step preprocessing functions can be used with any other platform.

### Value

A DataForPREDA object is returned.

### Author(s)

Francesco Ferrari

### See Also

`DataForPREDA`

### Examples

    ## Not run:

    require("PREDAsampledata")
    CELfilesPath <- system.file("sampledata", "GeneExpression",
    package = "PREDAsampledata")
    infofile <- file.path(CELfilesPath , "sampleinfoGE_PREDA.txt")
    sampleinfo<-read.table(infofile, sep="\t", header=TRUE)

    GEDataForPREDA<-preprocessingGE(SampleInfoFile=infofile,
    CELfiles_dir=CELfilesPath,
    custom_cdfname="hgu133plus2",
    arrayNameColumn=1,
    sampleNameColumn=2,
    classColumn="Class",
    referenceGroupLabel="normal",
    statisticType="tstatistic",
    optionalAnnotations=c("SYMBOL", "ENTREZID"),
    retain.chrs=1:22
    )

    ## End(Not run)

[Package PREDA version 1.40.0 Index]