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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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After I perform chromatographic peak detection, how do I confirm the quality of my peaks? #736

Open v-v1150n opened 7 months ago

v-v1150n commented 7 months ago

After I perform chromatographic peak detection, how do I confirm the quality of my peaks?

Previously, IPO kit could be used to find the best set of parameters for peak detection, but the IPO kit seemed to have some problems, so I wanted to directly test various possible parameters to perform peak detection. Is there any xcms-based kit or function be used?

jorainer commented 7 months ago

On what metrics would you base/assess the quality of the peaks? We have something on our TODO list (see issue #705), but did not yet progress on that.

what you could do (with base R commands) is evaluate the m/z and rt widths of the peaks that you detected (using the respective columns from the chromPeaks() matrix), or also count the number of peaks per sample etc. Also, visual inspection of either random peaks or compounds that you know are present in your data (by extracting their EIC) helps.