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| 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. |
| 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. |