# Cross Platform Meta-Analysis of Microarray Data

## Documentation for package ‘crossmeta’ version 1.19.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.