gSlide-class

getLayout,gSlide-method

initialize,gSlide-method

show,gSlide-method


A class repressent a slide used in experiment. Inherited from
Class <code>"gArray"</code>. The layout of the slide is descriped by a data
frame with columns of "rows", "columns", and "wells".


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

gSlide-class function

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

Objects from the Class

Extends

<dl>
    <dt>getLayout</dt><dd><code>signature(x = "gSlide")</code>: ... </dd> <dt>initialize</dt><dd><code>signature(.Object = "gSlide")</code>: ... </dd> <dt>show</dt><dd><code>signature(object = "gSlide")</code>: ... </dd> </dl> 

Methods

A class repressent a slide used in experiment. Inherited from
Class <code>"gArray"</code>. The layout of the slide is descriped by a data
frame with columns of "rows", "columns", and "wells".

gSlide-class: Class `"gSlide"`

Description

Arguments

Objects from the Class

Extends

Methods

Examples