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| 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 |