# Cross Platform Meta-Analysis of Microarray Data

## Documentation for package ‘crossmeta’ version 1.16.1

- 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.
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