It's not like a lemon or other citrus where the pith adds bitterness. In fact if you notice a lot of cooks using microplanes to grate it don't bother peeling it. As long as the skin is clean to being with, it doesn't really matter. What matters is that you are breaking up the ginger, whether you are slicing it, macerating it in a food processor or chunking it. It's about breaking it up. And the skin contains a lot of flavor and aroma that you want in there anyway.
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I peeled mine,just because charley said it would be earthy and taste bad if I didn't, but I think the fresher you buy it the better(get it like I did from the neighborhood asian store, its fresher and cheaper.)
If you slice the ginger into thick disks, peeling it is super easy with a paring knife. If you want to grate the ginger, it helps to partially freeze it first. A regular hand grater will make short order of partially frozen ginger.
I tried pealing and food processing, lots of work. Now I just wash it and then matchstick it with the peal on. I boil it and then let it cool over night. I can't tell the difference.
I cut it into chunks, then drop in boiling water for a few seconds. say about 30 sec. This should kill off any major nasties. Then I drop the chunks into the food proessesor. When it's chopped as finely as it will reasonably get, I add a little water. Then I hand squeeze all this through cheese cloth.. then strain it through a sieve.
I've also simmered the chunks in a little water (enough to cover) and let it cool (1st bring to a boil, then simmer). This water is added to the food processor and used in the brew. Doesn't taste as sharp as the raw. I'd experiment with both methods but either way - no need to peel.