PADOG (version 1.14.0)

filteranot: Remove duplicate probesets/probes from an gene expression matrix based on p-values from a moderated t-test, in order to apply a gene set analysis.

Description

This function helps to deal with multiple probesets/probes per gene prior to geneset analysis.

Usage

filteranot(esetm=NULL,group=NULL,paired=FALSE,block=NULL,annotation=NULL,include.details=FALSE)

Arguments

esetm

A matrix containing log transfomed and normalized gene expression data. Rows correspond to genes and columns to samples. Rownames of esetm need to be valid probeset or probe names.

group

A character vector with the class labels of the samples. It can only contain "c" for control samples or "d" for disease samples.

paired

A logical value to indicate if the samples in the two groups are paired.

block

A character vector indicating the block ids of the samples classified by the group variable, if paired=TRUE. The paired samples must have the same block value.

annotation

A valid chip annotation package name (e.g. "hgu133plus2.db")

include.details

If set to true, will include all columns from limma's topTable for this dataset.

Value

A data frame containing the probeset IDs (and corresponding ENTREZ IDs) of the best probesets for each gene ;

Details

See cited documents for more details.

References

Adi L. Tarca, Sorin Draghici, Gaurav Bhatti, Roberto Romero, Down-weighting overlapping genes improves gene set analysis, BMC Bioinformatics, 2012, submitted.

See Also

padog

Examples

#run padog on a colorectal cancer dataset of the 24 datasets benchmark GSE9348
set="GSE9348"
data(list=set,package="KEGGdzPathwaysGEO")
x=get(set)
#Extract from the dataset the required info
exp=experimentData(x);
dataset= exp@name
dat.m=exprs(x)
ano=pData(x)
design= notes(exp)$design
annotation= paste(x@annotation,".db",sep="")

dim(dat.m)
#get rid of duplicates in the same way as is done for PADOG and assign probesets to ENTREZ IDS
#get rid of duplicates by choosing the probe(set) with lowest p-value; get ENTREZIDs for probes
aT1=filteranot(esetm=dat.m,group=ano$Group,paired=(design=="Paired"),block=ano$Block,annotation) 

#filtered expression matrix
filtexpr=dat.m[rownames(dat.m)%in%aT1$ID,]
dim(filtexpr)