You are interested in understanding how the brain works, and are using the fruit fly Drosophila as a model system to study brain development. You perform microarray analysis to try to determine genes expressed in the fly brain. For your microarray experiment, you first prepare cDNA from fly brains and label it with a red fluorochrome. Then, you isolate cDNA from whole flies and label it with a green fluorochrome. Next, you hybridize these cDNA populations to a microarray containing the Drosophila genes. From this, you obtain a list of genes that are specifically enriched in the brain (those that show up as a red spot on the microarray).
You are disappointed because your favorite fly gene, tubby, does not appear on this list, even though you have repeated the microarray experiment 10 times and did not encounter any technical difficulties. The reason you thought tubby would appear on this list is that you believe tubby is important for brain development, since flies mutant in tubby have no brains. Not to be discouraged, you perform in situ analysis using the tubby DNA as a probe, and see that it is expressed at high levels in the fly brain of normal flies but not expressed in animals lacking the tubby gene.
Why do you think tubby did not show up as a gene specifically enriched in the brain in your microarray experiment?