plot-methods

plot,gExperimentSetup,missing-method


 Create bar plots based on the experiment setup.


methods

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

plot-methods function

<dl> <dt><code>signature(x = "gExperimentSetup", y = "missing")</code></dt><dd>
Plot distribution of relevant variables over different batches.
</dd> </dl>

Methods

Create bar plots based on the experiment setup.

plot-methods: Methods for Function `plot`

Description

Arguments

Methods