My data set has no “significant” genes, but when I run ermineJ with resampling I get significant gene sets. How do I interpret these results?
Carefully. ErmineJ’s resampling methods are based on analyzing your gene expression data in isolation, without reference to any theoretical background model (other methods may be added in future versions of ermineJ that allow this). It is capable of identifying the most interesting gene sets in your data, but this does not necessarily mean those gene sets are interesting in general. We recommend using such findings as an exploratory method for helping identify potential genes of interest, but because no gene is statistically significant on its own, the results for any given gene would have to be dealt with on a case-by-case basis using considerations other that statistical significance.
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