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Old 08-08-2014, 04:16 AM   #15
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Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

If you take a look at the GFOLD publication, for example, and the GFOLD documentation in BioConductor, it is more sophisticated than a simple Wilcoxon test. GFOLD represents one effort to deal with the (admittedly undesirable) situtation of not have any biological replicates, yet still attempt to maintain some rigor to how differentially expressed genes are selected.

People publish differential gene expression results based on nothing but fold change, but be prepared to fully justify why you did not include replication into your study design (e.g. sometimes, clinical studies, or any study using very difficult to obtain and/or highly limited samples are simply unable to include biological replicates). You would also be best to validate at least some of the genes, at least those critical to your final interpretation or conclusions, or you'll find you are required to anyway to get past peer review.

Given that there are published methods for making the most, statistically, from no or very few replicates, you would also be best to explore them, as a reviewer familiar with them will point them out to you if you do not.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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