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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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Duplicate values created by fillChromPeaks #750

Open frankyWk opened 1 month ago

frankyWk commented 1 month ago

Our workflow is findChromPeaks, groupChromPeaks and fillChromPeaks. I am finding duplicate values in the output from fillChromPeaks - I have attached a sample file. Is this expected behaviour where peaks are e.g. <1ppm apart and default FillChromPeaksParam() values are used? 3_peaks_after_filling_missing.csv

jorainer commented 4 weeks ago

fillChromPeaks() is only integrating values for features for which a chrom peak was missing in one or more files. So, it depends on the features that were defined. If you have features with less than 1 ppm apart then the function will integrate values for this. I guess you might have to check the settings for the groupChromPeaks() again.