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 .

AuthorLi Yan
Date of publicationNone
MaintainerLi Yan <li.yan@roswellpark.org>
LicenseArtistic-2.0
Version1.22.0
http://www.biomedcentral.com/1471-2164/13/689

View on Bioconductor

Functions

BeadChip96ToMSA4MAP Man page
BeadChip-class Man page
BeadPlate-class Man page
cid,gContainer-method Man page
create.experiment.setup Man page
create.optimized.setup Man page
dim,gArray-method Man page
exclude<- Man page
exclude<-,gContainer-method Man page
gArray-class Man page
gAssembly-class Man page
gc Man page
gContainer-class Man page
GenotypingChip Man page
get.experiment.setup Man page
get.gAssembly,gContainer-method Man page
get.gAssembly,gExperimentSetup-method Man page
getLayout Man page
getLayout,BeadChip-method Man page
getLayout,gArray-method Man page
getLayout,gAssembly-method Man page
getLayout,gContainer-method Man page
getLayout, gPlate-method Man page
getLayout,gSlide-method Man page
getLayout,MSAroboticPlate-method Man page
gExperimentSetup-class Man page
gPlate-class Man page
gs Man page
gSample-class Man page
gSetup Man page
gSetup2 Man page
gSlide-class Man page
IlluminaBeadChip Man page
IlluminaBeadChip24Plate Man page
IlluminaBeadChip48Plate Man page
IlluminaBeadChip96Plate 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
initialize,MSAroboticPlate-method Man page
map.to.MSA Man page
map.to.MSA Man page
map.to.MSA,data.frame,MSAroboticPlate-method Man page
map.to.MSA,data.frame,MSAroboticPlate-method Man page
map.to.MSA,gExperimentSetup,MSAroboticPlate-method Man page
map.to.MSA,gExperimentSetup,MSAroboticPlate-method Man page
metadata Man page
metadata<- Man page
metadata<-,gArray-method Man page
metadata,gArray-method Man page
metadata<-,gAssembly-method Man page
metadata,gAssembly-method Man page
metadata<-,gContainer-method Man page
metadata,gContainer-method Man page
metadata<-,gExperimentSetup-method Man page
metadata,gExperimentSetup-method Man page
MSA4.plate Man page
MSAroboticPlate-class Man page
multi.barplot Man page
multi.chisq.test Man page
ncol,gArray-method Man page
nrow,gArray-method Man page
optimal.block Man page
optimal.shuffle Man page
pheno Man page
plot,gExperimentSetup,missing-method Man page
plot,gExperimentSetup,missing-method Man page
plot-methods Man page
predefined Man page
QC Man page
samples,gExperimentSetup-method Man page
setup.container Man page
setup.sample 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
show,MSAroboticPlate-method Man page
summary Man page
summary,gExperimentSetup-method Man page
summary,gSample-method Man page

Files

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

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