When I rack to secondary (usually after a 14 day primary), I often notice yeast/protein flakes in the beer, it's most noticeable when I use Nottingham yeast. So far they've always settled out by the end of the 14 day secondary, and if I put the carboy somewhere cooler they seem to settle out faster. Let it ride in secondary for a couple of weeks and see if they don't settle out.
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Primary 2: Edwort's Robust Porter
Secondary 1: LW Pale Ale
Secondary 1: Blackened Soul RIS
Kegged: Dead Guy Ale
Kegged: Rye Pale Ale
Kegged: Haus Pale Ale
Kegged: Nut Brown Ale
Kegged: Afrikan Amber
Kegged: Jock Scott Ale
Kegged: Afrikan Amber
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