% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/pRRophetic.R

\name{homogenizeData}

\alias{homogenizeData}

\title{Take two expression matrices and return homogenized versions of the matrices.}

\usage{

homogenizeData(

  testExprMat,

  trainExprMat,

  batchCorrect = "eb",

  selection = -1,

  printOutput = TRUE

)

}

\arguments{

\item{testExprMat}{Gene expression matrix for samples on which we wish to predict a phenotype. Gene names as rows, samples names as columns.}

\item{trainExprMat}{Gene expression matrix for samples for which we the phenotype is already known.}

\item{batchCorrect}{The type of batch correction to be used. Options are "eb" for Combat, "none", or "qn" for quantile normalization.}

\item{selection}{parameter can be used to specify how duplicates are handled, by default value -1 means ask the user. 1 means summarize duplictes by their mean and 2 means to disguard all duplicate genes.}

\item{printOutput}{Set to FALSE to supress output}

}

\value{

a list containing two entries $train and $test, which are the homogenized input matrices.

}

\description{

This function accepts two expression matrices, with gene ids as rownames() and

sample ids as colnames(). It will deal with duplicate gene ids.

subset and order the matrices correctly.

and perform homogenize the data using whatever method is specified (by default Combat from the sva library).

}

\author{

Paul Geeleher, Nancy Cox, R. Stephanie Huang

}

\keyword{internal}