\name{getOrder}
\alias{getOrder}
\title{Order Probesets Based on Fold Change Values}
\description{
  This function is used to create a \code{list} containing the correct
  order to output a set of probesets based on the fold change values for
  those probesets. This is an internal function and is not intended to
  be called by end users.
}
\usage{
getOrder(fcList, order.by)
}
\arguments{
  \item{fcList}{A \code{list} of named lists, generally produced by a
    call to \code{makeFCList}}
  \item{order.by}{One of 'sum', 'max', 'median', or 'mean'. This orders
    the output for those tables that have multiple fold change values
    based on the summary statistic chosen. Defaults to 'sum'.}
}
\details{
  The purpose of this function is to come up with some ordering for
  probesets that will be ouput by a call to \code{vennSelectFC}. The
  ordering for probesets unique to a given comparison is simple, since
  there is only one fold change to be considered. However, when there
  are more than one comparison, we have to decide how the probesets
  should be ordered. The choices available include those that seemed
  reasonable to me when I wrote this function. Presumably there are
  other reasonable choices that may need to be included.
}
\author{James W. MacDonald <jmacdon@med.umich.edu>}
\keyword{internal}