How often does the Illumina Tech Support group encounter non-concordance between probes?
For genes that have differential expression scores of greater than 13 we virtually never see non-concordance. The fold change is usually very close. Keep in mind that differential expression scores are not fold change scores; the differential expression score is assigned to the gene based on the log value of its p-value. As is typical of other platforms, the two probes may vary in intensity based on sequence differences. We always average the fold changes from the two probes.
