she wrote the letter in pencil译为她用铅笔写的这封信,如果用by pencil语法角度有不同吗?

你好.记住以下结构,有助于你的学习：
write with a pen
write with a pencil -------- 有a / an就用with,强调书写工具
write in ink
write in pencil---------没有a / an, 就用 in,强调书写原料
如果是by,往往强调交通工具或通讯工具,注意没有a/an:
come by bus
go by plane
talk by phone
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