The question came up in a recent Google Webmaster Help forum post, and Aaseesh Marina from Google commented on the issue from the Google quality site of the issue when 50% of a site’s pages are noindexed.
Using noindex tag on x% of pages on your site doesn’t make the remaining pages bad. Google ranks each page on separately based on relevance, and other factors so you don’t have to worry about any thin content penalty.
So noindexing a mass number of pages won’t affect the quality of the indexed portion of the site, provided the noindex has been processed if those pages were recently changed to noindex. That said, if the remaining pages on the site that are indexed also have quality issues, then the site can still be impacted by both Panda and other quality algos Google uses in the search results.
Jennifer Slegg
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