add_adjusted            Add expression data adjusted for
                        pairs/surrogate variables
add_sources             Add sample source information for
                        meta-analysis.
add_vsd                 Add VST normalized assay data element to
                        expression set
bulkPage                Logic for Select Contrasts Interface
bulkPageUI              UI for Select Contrasts Interface
diff_expr               Differential expression analysis of esets.
es_meta                 Effect size combination meta analysis.
exprs.MA                Extract Log-Expression Matrix from MAList
filter_genes            Filter genes in RNA-seq ExpressionSet
fit_ebayes              Fit ebayes model
fix_illum_headers       Attempts to fix Illumina raw data header
get_raw                 Download and unpack microarray supplementary
                        files from GEO.
get_sva_mods            Get model matrices for surrogate variable
                        analysis
get_top_table           Get top table
get_vsd                 Get variance stabilized data for exploratory
                        data analysis
gs.names                Map between KEGG pathway numbers and names.
gslist                  KEGG human pathway genes.
ilmn.nnum               Count numeric columns in raw Illumina data
                        files
iqr_replicates          Removes features with replicated annotation.
load_agil_plat          Load Agilent raw data
load_diff               Load previous differential expression analyses.
load_raw                Load and annotate raw data downloaded from GEO.
makeExampleCountsEset   Make example ExpressionSet
open_raw_illum          Open raw Illumina microarray files.
phenoData.ch2           Construct AnnotatedDataFrame from Two-Channel
                        ExpressionSet
prefix_illum_headers    Run prefix on Illumina raw data files
remove_autonamed        Remove columns that are autonamed by data.table
run_limma               Linear model fitting of eset with limma.
run_limma_setup         Setup ExpressionSet for running limma analysis
run_sva                 Run surrogate variable analysis
setup_prev              Setup selections when many samples.
symbol_annot            Add hgnc symbol to expression set.
