getEIC gives wrong result for zero intensity scans about xcms HOT 4 CLOSED

getEIC works on the profile matrix, not the actual raw data while rawEIC directly extracts the values from the raw data. That might be the explanation (without having looked in detail yet).

This was completely confusing to me from the beginning and in the (not so far) future I would like to clear all these things/confusions.

from xcms.

Yeah I understand that. But what behaviour should I then expect with step / profStep = 0? What is it doing then?

from xcms.

Funny, with my xcms (version 1.49.3) I cannot use step = 0; that throws an error (due to mass <- seq(floor(mrange[1]/step)*step, ceiling(mrange[2]/step)*step, by = step)). So getEIC will always use the profile matrix as it would not accept a step which is 0.

I wouldn't spent too much time with that method, as this is one of the candidate-methods that have to be fixed.
My goal will be to have one method and that extracts raw EIC data. Which could then, in a second step be binned.

from xcms.

I'm closing the issue now - feel free to re-open if needed.

from xcms.