--- a
+++ b/man/homogenizeData.Rd
@@ -0,0 +1,38 @@
+% 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}