OSAT

OSAT: Optimal Sample Assignment Tool

Bioconductor version: Release (2.11)

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.

Author: Li Yan

Maintainer: Li Yan <li.yan at roswellpark.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("OSAT")

To cite this package in a publication, start R and enter:

    citation("OSAT")

Documentation

PDF	R Script	An introduction to OSAT
PDF		gSetupBlock.pdf
PDF		gSetupOptimal.pdf
PDF		Meth450_Tracking_Sheet_onepage.pdf
PDF		paired.pdf
PDF		random.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, DataRepresentation, Design, QualityControl, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 2.11 (R-2.15)
License	Artistic-2.0
Depends	methods,stats
Imports
Suggests	xtable, Biobase
System Requirements
URL
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