OSAT

OSAT: Optimal Sample Assignment Tool

Bioconductor version: Release (2.14)

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 .

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   Reference Manual
Text   NEWS

Details

biocViews DataRepresentation, ExperimentalDesign, QualityControl, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends methods, stats
Imports
Suggests xtable, Biobase
System Requirements
URL http://www.biomedcentral.com/1471-2164/13/689
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source OSAT_1.12.0.tar.gz
Windows Binary OSAT_1.12.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) OSAT_1.12.0.tgz
Mac OS X 10.9 (Mavericks)
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