Question: How to deal with multiple probes for same gene while obtaining the co-expressed genes
gravatar for ancient_learner
5.0 years ago by
ancient_learner610 wrote:


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.

cladist coexpressed microarray • 3.1k views
ADD COMMENTlink modified 5.0 years ago by Istvan Albert ♦♦ 81k • written 5.0 years ago by ancient_learner610
gravatar for Istvan Albert
5.0 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

This is not an uncommon problem see the following posts:

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Istvan Albert ♦♦ 81k
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