nudge: Normal Uniform Differential Gene Expression detection

Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)

Author
N. Dean <nemad@stat.washington.edu> and A. E. Raftery <raftery@stat.washington.edu>
Date of publication
None
Maintainer
N. Dean <nemad@stat.washington.edu>
License
GPL-2
Version
1.40.0

View on Bioconductor

Man pages

hiv
Microarray intensity expression levels for HIV type 1...
like
Microarray intensity expression levels for like-like data
neg.contr
Indicator of known truly non differentially expressed genes...
norm1a
Function for normalizing the mean of single replicate log...
norm1b
Function for normalizing the mean and variance (or just the...
norm1c
Function for normalizing the mean of...
norm1d
Function for normalizing the mean and variance of...
norm2c
Function for normalizing the mean of...
norm2d
Function for normalizing the mean and variance of...
nudge1
Function for normalizing data, fitting a normal-uniform...
nudge2
Function for normalizing data, fitting a normal-uniform...
pos.contr
Indicator of known truly differentially expressed genes in...

Files in this package

nudge/DESCRIPTION
nudge/NAMESPACE
nudge/R
nudge/R/norm1a.R
nudge/R/norm1b.R
nudge/R/norm1c.R
nudge/R/norm1d.R
nudge/R/norm2c.R
nudge/R/norm2d.R
nudge/R/nudge1.R
nudge/R/nudge2.R
nudge/build
nudge/build/vignette.rds
nudge/data
nudge/data/hiv.RData
nudge/data/like.RData
nudge/inst
nudge/inst/doc
nudge/inst/doc/nudge.vignette.R
nudge/inst/doc/nudge.vignette.Rnw
nudge/inst/doc/nudge.vignette.pdf
nudge/man
nudge/man/hiv.Rd
nudge/man/like.Rd
nudge/man/neg.contr.Rd
nudge/man/norm1a.Rd
nudge/man/norm1b.Rd
nudge/man/norm1c.Rd
nudge/man/norm1d.Rd
nudge/man/norm2c.Rd
nudge/man/norm2d.Rd
nudge/man/nudge1.Rd
nudge/man/nudge2.Rd
nudge/man/pos.contr.Rd
nudge/vignettes
nudge/vignettes/chicago.bst
nudge/vignettes/chicago.sty
nudge/vignettes/nudge.vignette.Rnw
nudge/vignettes/nudge.vignette.bib
nudge/vignettes/nvignplot1.pdf
nudge/vignettes/nvignplot2.pdf
nudge/vignettes/nvignplot3.pdf
nudge/vignettes/nvignplot4.pdf