add_adjusted            Add expression data adjusted for
                        pairs/surrogate variables
add_sources             Add sample source information for
                        meta-analysis.
ch2_subset              Subset for Paired Two-Channel ExpressionSet
diff_expr               Differential expression analysis of esets.
es_meta                 Effect size combination meta analysis.
exprs.MA                Extract Log-Expression Matrix from MAList
fix_illum_headers       Attempts to fix Illumina raw data header
get_ch2_mod             Get design matrix for two-channel array
get_raw                 Download and unpack microarray supplementary
                        files from GEO.
get_sva_mods            Get model matrices for surrogate variable
                        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.
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
query_ref               Get correlation between query and reference
                        signatures.
run_select_contrasts    Shiny gadget to upload groups and select
                        contrasts
run_sva                 Run surrogate variable analysis
setup_prev              Setup selections when many samples.
symbol_annot            Add hgnc symbol to expression set.
to_eset                 Convert limma object to ExpressionSet
to_ma                   Covert expression values to MAList
which_max_iqr           Get row indices of maximum IQR within
                        annotation groups
xls_to_txt              Covert .xls files to .txt
