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Old 09-13-2014, 11:00 AM   #86
bigmw
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GAGE accepts log fold changes or other test statistics from differential expression analysis. Yes, you need to set ref = NULL and samp = NULL in gage function when differential expression analysis is already done. Details are described in section 5-6 of the workflow toturial:
http://www.bioconductor.org/packages...eqWorkflow.pdf

Speaking of log fold changes, you must have some reference state. In your case, it can be one cell population or some virtual state of their combination. Please make sure you understand your upstream differential expression analysis.
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