While we believe in the perspicuity of scripture, we also must acknowledge that all scripture is not equally clear. Some passages are undeniably difficult to understand, and others appear to be contradictory. How are we to deal with these problem passages?

[O]ne place must be compared and collated with another; the obscurer places with the plainer or less obscure. For though in one place the words may be obscure, they will be plainer in another. For example, James, chap. 2, verse 21, affirms that Abraham was justified by works. The place is obscure, and seems to favour the papists. Whence, then, shall we know the true meaning of this passage? Why, we must compare it with the second verse of the fourth chapter of the Epistle to the Romans, and so it will readily appear how this place is to be understood. For Paul, in Rom. iv. 2, expressly says, that Abraham was not justified by works, because then he would have whereof to glory: and it is sufficiently plain that the apostle Paul is speaking, in that place, of the works which followed the call of Abraham: first, because he says, “Abraham believed God, and it was counted unto him for righteousness;” which every body knows to have taken place after his call: secondly, because afterwards he proceeds to the example of David, whom all know to have been a holy man, regenerated by the Spirit of God, and called by God. We must needs therefore confess that the term ‘justification’ is taken in different senses, unless we choose to suppose that the apostles are at variance, and pronounce contradictory declarations. In James, therefore, to be justified means to be declared and shewn to be just, as Thomas Aquinas himself confesses upon that place; but, in Paul, to be justified denotes the same as to be absolved from all sins, and accounted righteous with God.

—William Whitaker, Disputations on the Holy Scriptures (Soli Deo Gloria, 2005), 471–472.