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With existing group-test analysis methods such as GSEA [23] [24], the assertion is made that in order to be significant, the data distribution per gene is significantly shifted between the contrasted classes.
The genetic bases for freezing tolerance variation between the contrasted accessions F83005-5 and DZA045-5 have been identified using a quantitative trait locus (QTL) mapping approach [ 38].
Hence, given the substantial differences between the contrasted groups and the absence of any strong batch effect, we assumed that this scenario was optimal to compare pipelines and normalization methods.
We also suggest that one could even rank these genes for their possible relevance to a phenotype of interest between the contrasted classes as we showed for our pathway-ranking algorithms (Figure S1, Table S3, also see Materials And Methods section).
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