I have 2 microarray data sets with 6 replicates each. I wanted to identify tissue specific co-regulated genes. I have processed the array data using dchip. I have retained all the probes with their expression values in all replicates. I used it as an input for cladist that calculates the correlation between 2 genes based on their expression values. However as we all know that microarray will have different probes with different expression values for the same gene I get different correlation values for the same pair of genes in my output. Shall I consider all such pairs as different (as multiple probes refer to the different splicing event of the same gene) or shall I take Average of correlation values (which I believe is not very appropriate thing to do). or shall I consider the pair that gives maximum correlation value as the appropriate on? which method would be good? please advice me on this.