preprocessingGE: 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", "SAM" (SAM statistical score for differential expression), "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".

Value

A DataForPREDA object is returned.

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.

Examples

Run this code


## 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="gahgu133plus2",
# arrayNameColumn=1,
# sampleNameColumn=2,
# classColumn="Class",
# referenceGroupLabel="normal",
# statisticType="tstatistic",
# optionalAnnotations=c("SYMBOL", "ENTREZID"),
# retain.chrs=1:22
# )
# ## End(Not run)