If the query genome is unknown, a microarray cannot be made for a target species. Microarrays have DNA fragments of what you want to amplify on them. Those fragments must be known.
DNA microarrays are microscope slides that are printed with thousands
of tiny spots in defined positions, with each spot containing a known
DNA sequence or gene.
It is entirely possible that different cell-lines express the same genes at drastically different levels.
The proteinatlas provides data and analyses on differences between certain tissues or cell types / cell-lines.
If your cells are of the same line/tissue, then they might still differ dependent on the cell-cycle, age and external factors. There are ...
If I understand your question and graph correctly, your Y-axis is log(x/REF), where REF is some external standard. Your "Ref" on the x-axis you expect to be the same as REF, so that log(Ref/REF) "should be" zero, but you find it is not.
However, it looks like the mean(log(Ref/REF)) is still approximately zero. This is what I would expect: ...