These two system types have a number of similarities. However, you will need to install a window unit in each room, whereas ductless systems require a single outdoor unit with multiple, inconspicuous indoor air handlers. The biggest selling point for window ACs is its low upfront prices. However, they don't provide adequate comfort and they lack both efficiency and the ability to improve the quality of the indoor air - which isn't the case for ductless cooling designs. You should also note that window air conditioners tend to be quite loud, don't offer as much comfort, take up a lot of window space, and diminishes natural light.
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