OSAT

Package: OSAT
Type: Package
Title: OSAT: Optimal Sample Assignment Tool
Version: 1.20.0
Author: Li Yan
Maintainer: Li Yan <li.yan@roswellpark.org>
Depends: methods, stats
Suggests: xtable, Biobase
Description: 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 .
URL: http://www.biomedcentral.com/1471-2164/13/689
License: Artistic-2.0
Collate: AllClasses.R AllGenerics.R gAssembly-class.R gSample-class.R
gSetup-class.R gUtils.R
Packaged: 2016-05-04 04:37:01 UTC; biocbuild
biocViews: DataRepresentation, Visualization, ExperimentalDesign,
QualityControl
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'OSAT' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OSAT'
    finding HTML links ... done
    BeadChip-class                          html  
    BeadPlate-class                         html  
    MSAroboticPlate-class                   html  
    QC                                      html  
    create.optimized.setup                  html  
    example.setup                           html  
    gArray-class                            html  
    gAssembly-class                         html  
    gContainer-class                        html  
    gExperimentSetup-class                  html  
    gPlate-class                            html  
    gSample-class                           html  
    gSlide-class                            html  
    get.experiment.setup                    html  
    multi.barplot                           html  
    multi.chisq.test                        html  
    optimal.block                           html  
    optimal.shuffle                         html  
    plot-methods                            html  
    predefined                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OSAT)
Making 'packages.html' ... done