This function extract a non-redundant signcant gene set list, groups of redundant gene sets, and related data from gage results. Redundant gene sets are those overlap heavily in their effective member gene lists or core genes.
Run GAGE analysis to infer gene sets (or pathways, functional groups etc) that are signficantly perturbed relative to all genes considered. GAGE is generally applicable to essentially all microarray dta independent of data attributes including sample size, experimental layout, study design, and all types of heterogeneity in data generation.
This function is used to compare the results after running multiple rounds of GAGE analysis. It is frequently used after batch analysis using gagePipe, but may also be used after multiple runs of gage manually.
Function gagePipe runs mutliple rounds of GAGE in a batch without interference, and outputs signcant gene set lists in text format, heatmaps in pdf format, and save the results in RData format.
This function outputs and visualizes the expression data for seleted genes. Potential output files include: a tab-delimited text file, a heatmap in PDF format, and a scatter plot in PDF format.
These functions test for perturbation of gene sets relative to all genes in the microarray data. They are the testing module for gage and single array analysis workflow.
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