This pairwise differential expression (de) workfow report was generated using Searchlight 2 (<*SL2_version*>). The normalised expression matrix at <*ne_file_path*> was combined with the background file at <*background_file_path*>, retaining only the <*expression_set_size*> genes that were present in both, to create the "expression set". Per sample group mean expression values and standard devitations per gene were calulated using numpy.

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Next the differential expression table at <*de_file_path*> which compares the two sample groups <*de_numerator*> and <*de_denominator*>, was combined with the expression set, retaining only the <*differential_expression_set_size*> genes that were present in both, to create the "differential expression set". Next a list of significantly differentially expressed genes was generated from the differential expression set using the adjusted p threshold of <*de_padj*> and the absolute log2fold theshold of > <*de_log2fold*>. Finally, all plots were generated as described in the figure legends of this report, using the R script at /de/<*workflow_ID*>/plots/workflow.r, and as described in the figure legends of this report.

