OSAT: OSAT: Optimal Sample Assignment Tool
Version 1.24.0

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 .

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AuthorLi Yan
Bioconductor views DataRepresentation ExperimentalDesign QualityControl Visualization
Date of publicationNone
MaintainerLi Yan <li.yan@roswellpark.org>
LicenseArtistic-2.0
Version1.24.0
URL http://www.biomedcentral.com/1471-2164/13/689
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OSAT")

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

Functions

BeadChip-class Man page
BeadChip96ToMSA4MAP Man page
BeadPlate-class Man page
GenotypingChip Man page
IlluminaBeadChip Man page
IlluminaBeadChip24Plate Man page
IlluminaBeadChip48Plate Man page
IlluminaBeadChip96Plate Man page
MSA4.plate Man page
MSAroboticPlate-class Man page
QC Man page Source code
assign.sample.to.container Source code
assignWells Source code
average.2D Source code
barplot.gExperimentSetup Source code
block.strata.sampling Source code
cid,gContainer-method Man page
combineFactors Source code
create.experiment.setup Man page Source code
create.optimized.setup Man page Source code
create.random.setup Source code
dim,gArray-method Man page
exclude<- Man page
exclude<-,gContainer-method Man page
expLink Source code
expSetup Source code
fraction.strata Source code
gArray-class Man page
gAssembly-class Man page
gContainer Source code
gContainer-class Man page
gExperimentSetup-class Man page
gPlate-class Man page
gSample Source code
gSample-class Man page
gSetup Man page
gSetup2 Man page
gSlide-class Man page
gc Man page
get.experiment.setup Man page Source code
get.gAssembly,gContainer-method Man page
get.gAssembly,gExperimentSetup-method Man page
get.gContainer Source code
get.gSample Source code
getLayout Man page
getLayout, gPlate-method Man page
getLayout,BeadChip-method Man page
getLayout,MSAroboticPlate-method Man page
getLayout,gArray-method Man page
getLayout,gAssembly-method Man page
getLayout,gContainer-method Man page
getLayout,gSlide-method Man page
gs Man page
initialize,MSAroboticPlate-method Man page
initialize,gAssembly-method Man page
initialize,gContainer-method Man page
initialize,gExperimentSetup-method Man page
initialize,gPlate-method Man page
initialize,gSample-method Man page
initialize,gSlide-method Man page
map.to.MSA Man page Man page
map.to.MSA,data.frame,MSAroboticPlate-method Man page Man page
map.to.MSA,gExperimentSetup,MSAroboticPlate-method Man page Man page
metadata Man page
metadata,gArray-method Man page
metadata,gAssembly-method Man page
metadata,gContainer-method Man page
metadata,gExperimentSetup-method Man page
metadata<- Man page
metadata<-,gArray-method Man page
metadata<-,gAssembly-method Man page
metadata<-,gContainer-method Man page
metadata<-,gExperimentSetup-method Man page
multi.barplot Man page Source code
multi.chisq.test Man page Source code
ncol,gArray-method Man page
nrow,gArray-method Man page
optimal.block Man page Source code
optimal.shuffle Man page Source code
pheno Man page
plot,gExperimentSetup,missing-method Man page Man page
plot-methods Man page
predefined Man page Source code
random.assign Source code
random.setup Source code
remove.zeros Source code
removeWells Source code
samples,gExperimentSetup-method Man page
set.expSetup Source code
setup.container Man page Source code
setup.sample Man page Source code
show,MSAroboticPlate-method Man page
show,gAssembly-method Man page
show,gContainer-method Man page
show,gExperimentSetup-method Man page
show,gPlate-method Man page
show,gSample-method Man page
show,gSlide-method Man page
summary Man page
summary,gExperimentSetup-method Man page
summary,gSample-method Man page
wells Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/gAssembly-class.R
R/gSample-class.R
R/gSetup-class.R
R/gUtils.R
build
build/vignette.rds
data
data/example.setup.RData
data/predefined.RData
inst
inst/doc
inst/doc/OSAT.R
inst/doc/OSAT.Rnw
inst/doc/OSAT.pdf
inst/extdata
inst/extdata/samples.txt
man
man/BeadChip-class.Rd
man/BeadPlate-class.Rd
man/MSAroboticPlate-class.Rd
man/QC.Rd
man/create.optimized.setup.Rd
man/example.setup.Rd
man/gArray-class.Rd
man/gAssembly-class.Rd
man/gContainer-class.Rd
man/gExperimentSetup-class.Rd
man/gPlate-class.Rd
man/gSample-class.Rd
man/gSlide-class.Rd
man/get.experiment.setup.Rd
man/multi.barplot.Rd
man/multi.chisq.test.Rd
man/optimal.block.Rd
man/optimal.shuffle.Rd
man/plot-methods.Rd
man/predefined.Rd
vignettes
vignettes/Meth450_Tracking_Sheet.xls
vignettes/Meth450_Tracking_Sheet_onepage.pdf
vignettes/OSAT.Rnw
vignettes/gSetupBlock.pdf
vignettes/gSetupOptimal.pdf
vignettes/paired.pdf
vignettes/random.pdf
vignettes/randomizationPackage.bib
OSAT documentation built on May 20, 2017, 10:08 p.m.