You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
44 lines
2.0 KiB
44 lines
2.0 KiB
9 years ago
|
% 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}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|