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I know that heat energy can be calculated by $I^2 R t$. Therefore, it's directly proportional to resistance.

However,

$$I^2 R t = \frac{V^2}{R}t$$

In this case, won't the heat energy be inversely proportional to the resistance? Won't these 2 statements contradict each other?

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You are implicitly assuming that $I$ and $V$ are constant quantities. If one says that $x$ is proportional to $y$, it means $x = ay$ where $a$ is a constant.

But consider what happens when you change $R$: either $V$ or $I$, or both, change. They are not constant.

I think it would be better to say that power is proportional to $I^2$, with coefficient of proportionality $R$, and power is also proportional to $V^2$, with coefficient of proportionality $1/R$. Changing $I$ or $V$ does not affect the value of $R$ (not in simple analyses anyway).

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