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HEM (version 1.44.0)

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

Description

This package fits heterogeneous error models for analysis of microarray data

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Version

Version

1.44.0

License

GPL (>= 2)

Maintainer

HyungJun Cho

Last Published

February 15th, 2017

Functions in HEM (1.44.0)

am.tran.half

AM transformation for LPE
hem.fdr

FDR Evaluation
am.tran

AM transformation for LPE
base.error.Olig

Baseline error estimation for oligonucleotide arrays
boot.base.ASE.Olig

Baseline error bootstrap estimation for oligonucleotide arrays
boot.base.PSE.Olig

Baseline error bootstrap estimation for oligonucleotide arrays
quant.normalize

Quantile normalization
base.PSE.Olig

Baseline PSE estimation for oligonucleotide arrays
quant.norm

Quantile normalization
fixbound.predict.smooth.spline

Prediction using smoothing spine
nonpar.error.Olig

Baseline error nonparametric estimation for oligonucleotide arrays
remove.sig.genes

Remove significant genes
mubcp

Gene expression data for mouse B cell development
nonpar.no.error.Olig

Baseline error nonparametric estimation for oligonucleotide arrays
hem.null.one

Generation of null data
par.no.error.Olig

Baseline error parametric estimation for oligonucleotide arrays
permut

Permutation
par.error.Olig

Baseline error parametric estimation for oligonucleotide arrays
nonpar.rep.error.Olig

Baseline error nonparametric estimation for oligonucleotide arrays
hem.null.two

Generation of null data
base.error.Olig.quanOnly

Baseline error estimation for oligonucleotide arrays
hem

Heterogeneous Error Model for Identification of Differential Expressed Genes Under Multiple Conditions
hem.preproc

Preprocessing
quant.normal

Normalization
par.rep.error.Olig

Baseline error parametric estimation for oligonucleotide arrays
quant.normal2

Normalization
base.ASE.Olig

Baseline ASE estimation for oligonucleotide arrays
boot.base.error.Olig

Baseline error bootstrap estimation for oligonucleotide arrays
pbrain

Gene expression data for primate brains
hem.eb.prior

Empirical Bayes (EB) Prior Specification
hem.null.no

Generation of null data