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Consider these two expressions:

Once I am done with my assignment, I will go through the Calculus book.

Once I am done with my assignment, I will read the Calculus book.

Is there any difference in the meaning of these two expressions?

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There is some difference, I think. Oddly, I think the difference could go in two opposite directions. "Read" means just that read. But if you say I will "go through" a calculus book (no capital needed there, by the way) that implies (to me) that you will work substantially on the book, doing exercises etc.

On the other hand, if you say you will "go through" a popular book (as opposed to a text) that, to me, implies almost skimming.

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    NOAD lists one meaning of the phrasal verb go through as search through or examine carefully or in sequence. Even that definition has some of the same ambiguity you aptly point out in your answer. I would say that "go through the Calculus book" could mean skim (less attention than "read"), or work through (more attention than "read"), or even mean read (in other words, be used as a synonym). – J.R. Sep 14 '13 at 15:56
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    Absolutely. The same ambiguity applies to go over. – FumbleFingers Sep 14 '13 at 16:30
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    To "go through" something is to examine it from end to end, not necessarily thoroughly. For example, I would "go through" a pile of socks to find matching pairs. – BobRodes Sep 15 '13 at 20:03
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The phrase "go through" does not necessarily imply reading in any particular way. In fact, it is not a phrase that one would ordinarily expect to apply to reading at all, and it derives that sense only from its context. Even then, having established from context that it pertains to reading, it is ambiguous. The manner of reading it refers to might also be derived from its context.

"As soon as I scan look in this book for the information I'm trying to find, I'll go through that stack of books to see if i can find it." This doesn't imply deep reading of any sort.

"After I finish learning Algebra, I have to go through the calculus textbook." This implies from its context that one is involved in concentrated study.

So I wouldn't suggest using the phrase without providing a context in which it can be interpreted.

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