BeadChip-class

IlluminaBeadChip

GenotypingChip

getLayout,BeadChip-method


  A predefined class represent BeadChip from Illumina. Inherited from
  class <code>gSlide</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

BeadChip-class function

<code>IlluminaBeadChip</code>: A slide with 6 rows and 2 columns. The 12
  wells is numbered columns first. <code>GenotypingChip</code>: A slide with 12 rows and one column.

Predefined chips

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

Extends

<dl>
    <dt>getLayout</dt><dd><code>signature(x = "BeadChip")</code>: Return a data
  frame represent the layout of the chip. </dd> </dl> 

Methods

A predefined class represent BeadChip from Illumina. Inherited from
  class <code>gSlide</code>.

BeadChip-class: Class `"BeadChip"`

Description

Arguments

Predefined chips

Extends

Methods

Examples