On-chip replicates
Microarrays often have multiple spots for the same probe sequence. They are called on-chip replicates. The Subio Platform software takes the median of signals as default.
Multiple probes for the same genes.
Also, microarrays often have multiple probes for the same genes. Those probe sequences were chosen from different parts of the gene body. The expression patterns from the various probes of the same gene can behave differently.
The first reason is biological. If there splicing variants exist, they can show characteristic behaviors.
The other reason is experimental, and which is the nature of omics. If you have ever seen the results of tiling arrays or mappings of RNA-Seq, you notice that different parts of a gene are measured differently. The effect looks random, not systematic. Omics is not a scope to see the truth but shows us the shadow of the exact status.
Regardless, from the reasons above, it is not a good idea to get the typical expression pattern of the gene by averaging. They should be treated differently from the first reason. And averaging results in losing the chance of discoveries because it converges to not-moving.
So I recommend you pick up your favorite probes. Y ou know that omics is a tool to get the list of candidates. So it would be best if you are careful about false-negatives in this phase. Y ou will examine later by subsequent experiments on the candidates.