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


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Documentation for package ‘HEM’ version 1.32.0

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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 arrays
boot.base.error.Olig Baseline error bootstrap estimation for oligonucleotide arrays
boot.base.PSE.Olig Baseline error bootstrap estimation for oligonucleotide arrays
fixbound.predict.smooth.spline Prediction using smoothing spine
hem Heterogeneous Error Model for Identification of Differential Expressed Genes Under Multiple Conditions
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 arrays
nonpar.no.error.Olig Baseline error nonparametric estimation for oligonucleotide arrays
nonpar.rep.error.Olig Baseline error nonparametric estimation for oligonucleotide arrays
par.error.Olig Baseline error parametric estimation for oligonucleotide arrays
par.no.error.Olig Baseline error parametric estimation for oligonucleotide arrays
par.rep.error.Olig Baseline error parametric estimation for oligonucleotide arrays
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