BeadPlate-class

IlluminaBeadChip96Plate

IlluminaBeadChip48Plate

IlluminaBeadChip24Plate


A class represent a plate consistent of multiple chips. Inherite from
class <code>gPlate</code>. 


classes

A sizable genomics study such as microarray often involves
the use of multiple batches (groups) of experiment due to
practical complication. To minimize batch effects, a careful
experiment design should ensure the even distribution of
biological groups and confounding factors across batches. OSAT
(Optimal Sample Assignment Tool) is developed to facilitate the
allocation of collected samples to different batches. With
minimum steps, it produces setup that optimizes the even
distribution of samples in groups of biological interest into
different batches, reducing the confounding or correlation
between batches and the biological variables of interest. It
can also optimize the even distribution of confounding factors
across batches. Our tool can handle challenging instances where
incomplete and unbalanced sample collections are involved as
well as ideal balanced RCBD. OSAT provides a number of
predefined layout for some of the most commonly used genomics
platform. Related paper can be find at
http://www.biomedcentral.com/1471-2164/13/689 .

Li Yan

OSAT

OSAT: Optimal Sample Assignment Tool

BeadPlate-class function

Objects can be created by calls of the form <code>new("BeadPlate", chip, nRows, nColumns, comment, ...)</code>. 

Objects from the Class

<dl>
    <dt><code>chip</code>:</dt><dd>Object of class <code>"gSlide"</code>.  The slide used
      in the plate.</dd> <dt><code>nRows</code>:</dt><dd>Object of class <code>"integer"</code>. Number of
      clide per row. </dd> <dt><code>nColumns</code>:</dt><dd>Object of class <code>"integer"</code>. Number of
      slide per column. </dd> <dt><code>layout</code>:</dt><dd>Object of class <code>"data.frame"</code>. A data frame represent
          the layout of the plate.   </dd> <dt><code>byrow</code>:</dt><dd>Object of class <code>"logical"</code>. Order of
      slide on the plate. </dd> <dt><code>metadata</code>:</dt><dd>Object of class <code>"list"</code>.A brief description of the plate.  </dd> </dl> 

Slots

<code>IlluminaBeadChip96Plate</code> <code>IlluminaBeadChip48Plate</code> <code>IlluminaBeadChip24Plate</code> are plates that hold 2, 4, 8 <code>IlluminaBeadChip</code> chips and have 24, 48, 96 wells, respectively.

Predefined plate

Class <code>"gPlate"</code>, directly.
Class <code>"gArray"</code>, by class "gPlate", distance 2.

Extends

A class represent a plate consistent of multiple chips. Inherite from
class <code>gPlate</code>.

BeadPlate-class: Class `"BeadPlate"`

Description

Arguments

Objects from the Class

Slots

Predefined plate

Extends

Examples