OSAT: OSAT: Optimal Sample Assignment Tool

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
Date of publication
None
Maintainer
Li Yan <li.yan@roswellpark.org>
License
Artistic-2.0
Version
1.22.0
URLs

View on Bioconductor

Man pages

BeadChip-class
Class '"BeadChip"'
BeadPlate-class
Class '"BeadPlate"'
create.optimized.setup
Create optimized setup
example.setup
R data object based on example file.
gArray-class
Class '"gArray"'
gAssembly-class
Class '"gAssembly"'
gContainer-class
Class '"gContainer"'
get.experiment.setup
Get experiment assignment after optimization.
gExperimentSetup-class
Class '"gExperimentSetup"'
gPlate-class
Class '"gPlate"'
gSample-class
Class 'gSample'
gSlide-class
Class '"gSlide"'
MSAroboticPlate-class
Class '"MSAroboticPlate"'
multi.barplot
multi.barplot
multi.chisq.test
multi.chisq.test
optimal.block
optimal.block
optimal.shuffle
optimal.shuffle
plot-methods
Methods for Function 'plot'
predefined
Show predefined objects in the package.
QC
QC

Files in this package

OSAT/DESCRIPTION
OSAT/NAMESPACE
OSAT/NEWS
OSAT/R
OSAT/R/AllClasses.R
OSAT/R/AllGenerics.R
OSAT/R/gAssembly-class.R
OSAT/R/gSample-class.R
OSAT/R/gSetup-class.R
OSAT/R/gUtils.R
OSAT/build
OSAT/build/vignette.rds
OSAT/data
OSAT/data/example.setup.RData
OSAT/data/predefined.RData
OSAT/inst
OSAT/inst/doc
OSAT/inst/doc/OSAT.R
OSAT/inst/doc/OSAT.Rnw
OSAT/inst/doc/OSAT.pdf
OSAT/inst/extdata
OSAT/inst/extdata/samples.txt
OSAT/man
OSAT/man/BeadChip-class.Rd
OSAT/man/BeadPlate-class.Rd
OSAT/man/MSAroboticPlate-class.Rd
OSAT/man/QC.Rd
OSAT/man/create.optimized.setup.Rd
OSAT/man/example.setup.Rd
OSAT/man/gArray-class.Rd
OSAT/man/gAssembly-class.Rd
OSAT/man/gContainer-class.Rd
OSAT/man/gExperimentSetup-class.Rd
OSAT/man/gPlate-class.Rd
OSAT/man/gSample-class.Rd
OSAT/man/gSlide-class.Rd
OSAT/man/get.experiment.setup.Rd
OSAT/man/multi.barplot.Rd
OSAT/man/multi.chisq.test.Rd
OSAT/man/optimal.block.Rd
OSAT/man/optimal.shuffle.Rd
OSAT/man/plot-methods.Rd
OSAT/man/predefined.Rd
OSAT/vignettes
OSAT/vignettes/Meth450_Tracking_Sheet.xls
OSAT/vignettes/Meth450_Tracking_Sheet_onepage.pdf
OSAT/vignettes/OSAT.Rnw
OSAT/vignettes/gSetupBlock.pdf
OSAT/vignettes/gSetupOptimal.pdf
OSAT/vignettes/paired.pdf
OSAT/vignettes/random.pdf
OSAT/vignettes/randomizationPackage.bib