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.

Author
Raphael Gottardo
Date of publication
None
Maintainer
Raphael Gottardo <raph@stat.ubc.ca>
License
GPL (>= 2)
Version
1.48.0

View on Bioconductor

Man pages

arrange.row
Reorder a dataset by increasing row order.
est.shift
Estimate the shift used in the log transformation
fit.model
Robust estimation of microarray intensities with replicates
hiv
Cellular gene expression upon human immunodeficiency virus...
is.row.na
Test if a matrix contains missing values
ls.effect
Compute the least squares estimates of the all the effects of...
mat.mean
Compute the mean and standard deviation of each row in a data...
ratio.plot
Plot the estimated log ratios against the overall intensities
weight.plot
Plot the weights of a given array using the spatial location...

Files in this package

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