I'm using publicly available microarray data for finding correlations in gene expression. I am a novice in microarray data analysis and usage. As I understand, microarray data is better used for differential analysis and cannot be used as a surrogate for absolute expression. But it seems logical for me, that changes in signal intensity across conditions can be used for finding expression correlations between genes. Am I wrong in assuming this?

In order to do this, I also require unique expression vectors from each gene. But as I understand about Illumina Beadchip data, there are multiple copies of a probe associated to a gene (probably signifying different regions of gene). So which expression vector to choose for representing expression of a gene? I also do not have bead level data for summarizing gene expression for my chosen experiment, as I am using publicly available data.

Please help. Thanks