"In your desk" implies that something is physically located inside your desk. For example:
* "I found my lost pen in my desk."
* "There are some important documents in your desk."
"From your desk" implies that something is originating from your desk or you are moving something away from your desk. For example:
* "Can you please take this file from my desk to the printer?"
* "I'm working from my desk all day today."
It's important to consider the meaning you want to convey and choose the preposition accordingly.