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What is causing noise

Exposure compensation is a feature when in shutter priority mode that will allow you to sort of tweak the cameras judgement so that it will choose settings slightly over or under ( or excessiveley if you choose ) the actual proper exposure for that given metering mode. Check and make sure that ISO is not in "Auto" mode by mistake. Or check the metadata of the file ( right click and properties ) and make sure that it actually was captures at ISO 100. You may THINK it was set to that and in fact it wasn't. My initial hunch though, given that the smaller shots don't look too noisy, is that you are putting too much stock into the 100% viewing. There are things that can help avoid or reduce noise like I stated with the exposure stuff, but you just have to accept that there will be noise at 100% on that camera. I have a Canon 7D and 99.9% of the time, I reduce noise slightly in Adobe Camera Raw,and thats a camera that handles noise better than a D3000 and costs about 4 times as much.
 

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