Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. A user interface makes it easy to select control and treatment samples for each contrast and study. This input is used for subsequent surrogate variable analysis (models unaccounted sources of variation) and differential expression analysis. Final meta-analysis of differential expression values can include genes measured in only a subset of studies.
|Date of publication||None|
|Maintainer||Alex Pickering <email@example.com>|
|License||MIT + file LICENSE|
contribute: Contribute results of meta-analysis to public database.
diff_expr: Differential expression of esets.
es_meta: Effect size combination meta anaylsis.
get_raw: Download and unpack microarray supplementary files from GEO.
load_diff: Load previous differential expression analysis.
load_raw: Load and annotate raw data downloaded from GEO.
open_raw_illum: Open raw Illumina microarray files.
setup_prev: Setup selections when many samples.
symbol_annot: Add hgnc symbol to expression set.