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Old 08-28-2015, 06:06 AM   #88
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Heatmaps from sigGeneSet function show the perturbations of whole gene sets or pathways (in experiment samples vs controls). It is only meaningful for exmperiment samples, you donít really expect controls receive such perturbation score.
The gene set level heatmap is actually a unique feature of GAGE. Because it conducts a pair-wise comparison between experiment samples and controls. Therefore, we can have a gene set level test statistics (or p-values) for each experiment sample. The global statistics and p-values are then summarized from these individual tests. These stats/p-values are all included in the gage function output. You may check the paper for details of the statistical tests.
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