HEM: Heterogeneous error model for identification of differentially expressed genes under multiple conditions

This package fits heterogeneous error models for analysis of microarray data

Author
HyungJun Cho <hcho@virginia.edu> and Jae K. Lee <jaeklee@virginia.edu>
Date of publication
None
Maintainer
HyungJun Cho <hcho@virginia.edu>
License
GPL (>= 2)
Version
1.46.0
URLs

View on Bioconductor

Man pages

am.tran
AM transformation for LPE
am.tran.half
AM transformation for LPE
base.ASE.Olig
Baseline ASE estimation for oligonucleotide arrays
base.error.Olig
Baseline error estimation for oligonucleotide arrays
base.error.Olig.quanOnly
Baseline error estimation for oligonucleotide arrays
base.PSE.Olig
Baseline PSE estimation for oligonucleotide arrays
boot.base.ASE.Olig
Baseline error bootstrap estimation for oligonucleotide...
boot.base.error.Olig
Baseline error bootstrap estimation for oligonucleotide...
boot.base.PSE.Olig
Baseline error bootstrap estimation for oligonucleotide...
fixbound.predict.smooth.spline
Prediction using smoothing spine
hem
Heterogeneous Error Model for Identification of Differential...
hem.eb.prior
Empirical Bayes (EB) Prior Specification
hem.fdr
FDR Evaluation
hem.null.no
Generation of null data
hem.null.one
Generation of null data
hem.null.two
Generation of null data
hem.preproc
Preprocessing
mubcp
Gene expression data for mouse B cell development
nonpar.error.Olig
Baseline error nonparametric estimation for oligonucleotide...
nonpar.no.error.Olig
Baseline error nonparametric estimation for oligonucleotide...
nonpar.rep.error.Olig
Baseline error nonparametric estimation for oligonucleotide...
par.error.Olig
Baseline error parametric estimation for oligonucleotide...
par.no.error.Olig
Baseline error parametric estimation for oligonucleotide...
par.rep.error.Olig
Baseline error parametric estimation for oligonucleotide...
pbrain
Gene expression data for primate brains
permut
Permutation
quant.norm
Quantile normalization
quant.normal
Normalization
quant.normal2
Normalization
quant.normalize
Quantile normalization
remove.sig.genes
Remove significant genes

Files in this package

HEM/DESCRIPTION
HEM/NAMESPACE
HEM/R
HEM/R/hem.R
HEM/R/hem.eb.prior.R
HEM/R/hem.error.no.R
HEM/R/hem.error.one.R
HEM/R/hem.error.two.R
HEM/R/hem.fdr.R
HEM/R/hem.lpe.R
HEM/R/hem.null.no.R
HEM/R/hem.null.one.R
HEM/R/hem.null.two.R
HEM/R/hem.preproc.R
HEM/build
HEM/build/vignette.rds
HEM/data
HEM/data/mubcp.RData
HEM/data/pbrain.RData
HEM/inst
HEM/inst/doc
HEM/inst/doc/HEM.Rnw
HEM/inst/doc/HEM.pdf
HEM/man
HEM/man/am.tran.Rd
HEM/man/am.tran.half.Rd
HEM/man/base.ASE.Olig.Rd
HEM/man/base.PSE.Olig.Rd
HEM/man/base.error.Olig.Rd
HEM/man/base.error.Olig.quanOnly.Rd
HEM/man/boot.base.ASE.Olig.Rd
HEM/man/boot.base.PSE.Olig.Rd
HEM/man/boot.base.error.Olig.Rd
HEM/man/fixbound.predict.smooth.spline.Rd
HEM/man/hem.Rd
HEM/man/hem.eb.prior.Rd
HEM/man/hem.fdr.Rd
HEM/man/hem.null.no.Rd
HEM/man/hem.null.one.Rd
HEM/man/hem.null.two.Rd
HEM/man/hem.preproc.Rd
HEM/man/mubcp.Rd
HEM/man/nonpar.error.Olig.Rd
HEM/man/nonpar.no.error.Olig.Rd
HEM/man/nonpar.rep.error.Olig.Rd
HEM/man/par.error.Olig.Rd
HEM/man/par.no.error.Olig.Rd
HEM/man/par.rep.error.Olig.Rd
HEM/man/pbrain.Rd
HEM/man/permut.Rd
HEM/man/quant.norm.Rd
HEM/man/quant.normal.Rd
HEM/man/quant.normal2.Rd
HEM/man/quant.normalize.Rd
HEM/man/remove.sig.genes.Rd
HEM/src
HEM/src/hem.c
HEM/src/random4f.h
HEM/vignettes
HEM/vignettes/HEM.Rnw