Others may find your posting understandable. I don't. Please clarify:

By what sort of decision chain/data testing do we get to an output for  gene a.... that includes   gene_A sample_2 when there is no  gene_A sample_2 in the original data? I infer that it is not because the original data has two  geneA... entities because the  geneC sample...< /c> data do <b>NOT>/b> include 3 distinct data points to justify the<c> gene_C sample_3 output.

Minor update, mostly to offset data citations more clearly