rama: Robust Analysis of MicroArrays

Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rama")
AuthorRaphael Gottardo
Bioconductor views Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerRaphael Gottardo <raph@stat.ubc.ca>
LicenseGPL (>= 2)
Version1.50.0

View on Bioconductor

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/arrange.row.R R/est.shift.R R/fit.model.R R/is.row.na.R R/ls.effect.R R/mat.mean.R R/ratio.plot.R R/weight.plot.R
build
build/vignette.rds
data
data/hiv.R
inst
inst/doc
inst/doc/rama.R
inst/doc/rama.Rnw
inst/doc/rama.pdf
man
man/arrange.row.Rd man/est.shift.Rd man/fit.model.Rd man/hiv.Rd man/is.row.na.Rd man/ls.effect.Rd man/mat.mean.Rd man/ratio.plot.Rd man/weight.plot.Rd
src
src/estimation_slice.c
src/ex_estimation_slice.c
src/mean.sd.c
src/reorder.c
src/util.c
src/util.h
vignettes
vignettes/chicago.bst
vignettes/chicago.sty
vignettes/rama.Rnw
vignettes/robust_estimation.bib

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