i want to compare expression levels with the differential search tool form the human microarray platform (Microarray Data :: Allen Brain Atlas: Human Brain).
The number of analyzed probes varies when i change the contrast structure.
When i compare CA1 to CA3 i obtain 31384 analyzed probes, but when i compare CA1 to the whole brain i obtain 26991 analyzed probes.
What happens to the ~4000 probes that are not taken into account and why aren’t they taken into account.
Best wishes and thanks in advance
The differential expression tool for all of our gene expression atlases performed a differential search by comparing a target structure against a contrast structure, and returns genes with higher expression in the target structure, which means that every search will return a fraction of the genes (typically 40-60%, but not always). There are ~60,000 probes on the microarray and so the numbers you get back in your search make sense. If you instead want to find genes with higher expression in CA3 than CA1 (or with higher expression in whole brain than CA1), you’ll want to click on the circle arrow button to the right of the filter boxes to switch the target and contrast regions:
Thanks @jeremyinseattle, problem solved!
Makes totally sense and all of the probes are found!