If you're doing that from user space, the noise will be from scheduling delays as Linux context-switches your process to run other stuff.
You can minimise that type of effect thru use of cpu-affinity but not get rid of it completely.
A company I'm working was getting awful SFDR values on a 12-bit DAC and not meeting requirements, which I didn't loosen up on. It turns out that they were using linux userspace to set the values for rapid bringup and moving to a bare metal application fixed it up. 250 times a second linux interrupts were causing delayed samples.