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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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Bad practices with peak merging #724

Closed jmorim closed 3 months ago

jmorim commented 4 months ago

This has always bothered me in the vignette. These are two distinct chromatographic peaks that happen to share an m/z, so probably isomers. Why does the vignette suggest merging the two peaks?

https://github.com/sneumann/xcms/blob/48ac5e0cd983b34437719063d1327c452f2d29af/vignettes/xcms.Rmd#L485C1-L496C1

jorainer commented 3 months ago

that's a fair comment. this is just an example to show how such peaks could be joined, we don't say the should be. This is just to illustrate the effect of the minProp parameter. I will update the vignette to make it more clear.

jorainer commented 3 months ago

I've updated the description in the vignette now. Thanks for the feedback!

Feel free to reopen the issue if further changes are necessary