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I have one link unit above my navigation which targets exact keywords on what my site is about, on contrary my AdSense for content Leaderboard and Wide Skyscraper show ads that are totally opposite from my keyword, while my ctr increased for about 10 times with link unit I noticed CPC is lower also (but that was just based on one day, today is higher).

Is it so bad to completely get rid of standard content ads and put link units, because this way I earn so little for that site but I think that is because smart pricing (accidental clicks on ads that my users are not interested)?

I earn in whole day with about 25-35 clicks as much as keyword tool shows for only one click, my site is first for the topic? I really don't know what to do. Has anyone had similar situation or can give some advice?

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AdSense revenue vary by so many factors that it's hard to say if your income would be positively affected.

My first advice is just. Test it. Remove the Leaderboard & Skyscraper Ads and check by yourself how things will going.

P.S.: it's almost normal that your revenue is so little in comparison of the values provided by the keyword tool, since it's showing the price for AdWords (= for the advertisers) and not the AdSense revenue (= for the publishers). As you know Google makes money thanks to that gap.

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Keep in mind that users have to click twice on link units before you get paid. From AdSense Help, Ad CTR:

For link units, the number of ad clicks divided by the number of impressions for the page of ads that appears when a link unit is clicked.

The CTR reported for link units is completely different than CTR for other AdSense units and can't be compared.

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