First, consider the question without a negative:
Did you go to the store?
This question is asking if you did go to the store. Therefore, 'yes' and 'no' are respectively answers of
[Yes,] I did go to the store
and
[No,] I didn't go to the store.
You answer 'yes' to indicate that the statement "you did go to the store" is true; 'no' indicates that this statement is false.
The question you wish to answer asks for the negation of this statement
Since the question is now
Did you not go to the store?
you are now answering for the statement "you did not go to the store."
If this statement is true, then you answer yes.
However, as other answers have pointed out, a question phrased this way often displays or conveys a certain expectation, and sometimes isn't even meant as a question. This may be where the uncertainty in how to answer comes from.
Therefore, a full answer that addresses any ambiguity caused by expectations or implications would be
Yes, I did not go to the store.
or the negation,
No, I did go to the store.
(which you might consider as "I didn't not go to the store," which can be difficult to understand for some.)
If you were then to answer the question with solely 'yes' or 'no', you would say 'yes' if you did, in fact, go to the store.
For those unconvinced, consider how one would go about asking for the negation of a question if not in precisely this way - and if the trouble would be worth that interpretation.
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Does this answer your question? How to answer a negative question in English?
– None – 2020-01-01T15:54:28.390This is really interesting question! And link from @user2684291 is really useful. By my understanding the best way to answer more fully like "Yes, I didn't." or "No, I didn't." because of (as I just suppose) short form of answer "Yes" or "No" has potential to confuse your partner of dialogue anyway. This isn't depend on are native speaker your partner or aren't. This is question of nature of human mind with negative language structures. – sayfriend – 2020-01-01T17:00:39.073
@sayfriend: I don't agree that there's any possibility of confusion or misunderstanding. The only significance of negating *not* in the question is to convey the fact that *either at time of asking, or at some prior time*, the asker had reason to suppose the addressee *would* have gone to the store (where the non-negated form implies nothing about what the asker might expect). The *actual* answer to any such question would always be framed as if the question *hadn't* been negated. So *No* means No, I didn't go, and *Yes* means *Actually, yes - I did go*. – FumbleFingers Reinstate Monica – 2020-01-01T17:50:11.843
1Note that colloquial *Irish* commonly employs this kind of "negated question" in contexts where it's a kind of rhetorical question used to make a "slightly surprising" assertion. *I had a fight with Pat lat week, but I saw him in the pub last nigh, and didn't he buy me a pint? Fine fellow, that Pat is!* Where *Didn't X happen?* means *Although it might be hard to believe, X happened*. – FumbleFingers Reinstate Monica – 2020-01-01T18:48:34.790
@FumbleFingers: Well, obviously you’re not a mathematician. It seems obvious to me that, if you invert the sense of a question, you invert the answer. For example, “Is x < 5?” and “Is x ≥ 5?” Likewise, since the “inside” set and the “outside” set are complements, I perceive “not inside” as being equivalent to “outside”. So “Is the cat not in?” is equivalent to “Is the cat out?” – Scott – 2020-01-03T05:22:43.347
1@Scott: Well, obviously you’re not a linguist! :) It seems obvious to me that language works the way people actually use it, not the way mathematicians and logicians might think it should. Consider how many times someone has said Don't you know I love you?, and got the reply Of course! I venture to suggest that in every case, that reply would be short for *Of course I do know that*, not *I don't*. Natural language isn't exactly the same as the language of mathematics or formal logic systems. – FumbleFingers Reinstate Monica – 2020-01-03T14:08:38.957
1@sayfriend You're right. It's almost meaningless to answer with a simple yes or no because it's unclear what each of these is referring to, although I believe a possible answer here is in fact no, meaning "I didn't go". Yes, on the other hand, is not idiomatic, and I think it would mean the same thing as no. Yes would be idiomatic if it were followed by I did, with some emphasis perhaps. It's also possible to say the same thing using a no: Did you not go to the store? ~ No (emphatically), I did (also maybe emphatically) go. There are variations in tone and emphasis, though. – None – 2020-01-03T15:47:00.123
@Scott You cannot even in logic "invert the sense of a question"? "Is 5 < x" permits two contradictory answers: "5 is less than x" or "5 isn't less than x." A question does not assert a truth. "Isn't 5 < x" permits the exact same contradictory answers: "5 is less than x" or "5 isn't less than x." The only problem arises as to how to interpret the abbreviated response "yes" and "no.". English elects to interpret those abbreviations without regard to how the question is phrased. It uses "no " if the full response contains "not." It uses "yes" otherwise. – Jeff Morrow – 2020-01-04T22:32:33.323
@JeffMorrow: And that, more or less, is the point I was making: people who speak English have elected to use “Did you not go to the store?” to mean the same thing as “Did you go to the store?”, aside from some connotations and implications — and the fact that the former, despite having the form of a yes-or-no question, cannot be unambiguously answered with “yes” or “no”. It’s an arbitrary convention, devoid of logic. And FumbleFingers is the only person on this page who doesn’t understand that the “yes” and “no” answers are ambiguous. – Scott – 2020-01-04T23:40:57.897
@Scott No. Definitions and conventions are not devoid of logic. In the one-point compactification of the real numbers, plus and minus are arbitrary, which is different from illogical. You can make a completely consistent logical development whether you say minus is less than zero or greater than zero. Abelian groups are not "illogical" because non-abelian groups can be conceived. Logically consistent systems always depend eventually on arbitrary postulates. I can build a logically consistent algebra from a+b always equals b+a or from a+b does not always equal b+a. – Jeff Morrow – 2020-01-05T03:16:45.333