Updated master to SVN trunk revision 572

2015-06-26 15:04:35 -05:00
parent 67544a10e6
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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/normalize.and.transform.R
+\name{normalize.ODs}
+\alias{normalize.ODs}
+\title{Normalize OD readings for an entire array of well objects}
+\usage{
+normalize.ODs(well.array, normalize.method = "default", blank.value = NULL,
+  start.index = 2, add.constant = 1)
+}
+\arguments{
+\item{well.array}{an array of well objects.}
+
+\item{normalize.method}{see Details}
+
+\item{blank.value}{user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well.}
+
+\item{start.index}{which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
+
+\item{add.constant}{add a numeric constant to all timepoints in all wells.}
+}
+\description{
+Normalize OD readings for an entire array of well objects
+}
+\details{
+Note: This function does not write any new OD values to the well objects in the array - it only
+  fills the "norm" slot of each well object in the array with a value that will be subtracted
+  from all OD measurements when returning data from the wells using the function <data.from> (see well.class.R)
+
+ These functions make use of <raw.data> which simply returns the raw time and OD of a well (also see well.class.R)
+
+ note this is the only normalization function that acts on an entire array instead of an individual well.
+
+ normalize.method settings:
+ \describe{
+ \item{default}{subtracts the blank OD (either specified by <blank.value> or taken from the first timepoint as default)
+ of each well from all timepoints in that well}
+ \item{average.blank}{subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate}
+ \item{average.first}{takes the mean of the difference between the OD of the specified <start> timepoint and the first timepoint of all wells on a plate
+                    and subtracts this value from all timepoints in all wells on that plate}
+ \item{anything else}{do nothing}
+ }
+}
+