Cross Platform Meta-Analysis of Microarray Data

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Documentation for package ‘crossmeta’ version 1.31.0

• 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.
makeExampleCountsEset	Make example ExpressionSet
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.