PGR and breast cancer: Another reason for discrepancies in ER, PR, and HER2 assessment using both methods, as well as misclassification of breast cancer molecular subtyping using both methods, is that IHC may be biased in favour of selected or representative tumor areas, whereas endpoint RT-PCR gene expression assays frequently analyse gene levels in the entire tumor mass (which is a reflection of the average gene expression in the entire tissue slice) [34,42,43].