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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Correspondence: parameters set-up #550

Closed gmhhope closed 3 years ago

gmhhope commented 3 years ago

Dear XCMS developers,

This is the image of correspondence result with bw = 30; When I set a smaller bw values, the feature peaks can be distinguished.

However, I do want to know what will be the best practice for optimizing this value including many other critical correspondence parameters. Could you suggest anything?

Many thanks, Minghao Gong

image

jorainer commented 3 years ago

I ususally extract chromatograms for m/z ranges where I know that compounds are either co-eluting or eluting one after the other and then tune the bw setting on those signals with the help of the plotChromPeakDensity function (trying to separate them as good as possible).

You can also have a look here (or here for the rendered version) for some additional explanations and examples.

gmhhope commented 3 years ago

Thanks very much!

Oh I don't know there is a rendered version. I have already put your tutorial into Rmd myself. Thanks for letting me know. I will take a look at those! Thanks very much for your assistance!

Best, Minghao Gong

jorainer commented 3 years ago

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