The synthesis and purification of an oligonucleotide is a very complicated process with hundreds of individual steps. The overall success of a synthesis can depend on changes in minor amounts of contaminates from synthesis to synthesis, or even on uncontrollable variables such as the humidity level on the day of your particular synthesis, despite our environmental control systems. All of these (and other factors) can affect the amount that can be isolated of a particular compound with the proper purity.