Johannes Rainer

Looks good to me! I think the `ParamList` containing the parameter classes for the 3 steps is a not too bad idea (could be called `xcmsParam`). And the `YamsParam` that...

> What about moving XCMSnExp to MSnbase and possibly renaming it FeatureMSnExp, QuantMSnExp, ... and use it as XCMSnExp in xcms. I can't do it the other way due to...

Is it possible to have the same object with two different names? Also here, I don't have any strong feeling regarding the name of the object - `XCMSnExp` is very...

Ah, and here comes the trouble: I have a `[` method implemented that we would have to adopt: ```r #' @description The \code{[} method allows to subset a \code{\link{XCMSnExp}} #'...

Looks good to me. So, you're moving the `MsFeatureData` to `MSnbase`, right?

Some potential explanations Pablo that might help understanding the `snthresh`, in particular for peak detection on EIC - but be aware that I'm not the original developer of the algorithm,...

Hm, actually, I can not reproduce your example, as `plot(chr_raw)` on the 211201s013.mzXML file and your EIC extraction above gives me this:  i.e. there is absolutely no peak in...

Hm, actually, I can not reproduce your example, as `plot(chr_raw)` on the 211201s013.mzXML file and your EIC extraction above gives me this:  i.e. there is absolutely no peak in...

Yes, now I also get the EIC. But as you see, estimating the *noise* in such an EIC is pretty hard, because there is not much of a noise or...

the `diffreport` is not available for `XCMSnExp` objects. With the updated workflow it's now suggested to call `quantify` on the results `XCMSnExp` which returns a `SummarizedExperiment` object (standard data container...