I am searching public data series in GEO to look into differential gene expression for a particular gene in the context of schizophrenia. For my gene of interest, there are two different probes; one is sense and the other is antisense for the same region of the gene. Expression values for each of the two probes differ widely between available data series, i.e. in certain data series the antisense probe gives much higher expression values, while in others the sense one gives higher expression values.
Looking at the direction of the gene, one would assume that values from the sense probe should be used, however this discrepancy is a problem.
Could anyone help with an explanation please?