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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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Missing a few intensities information #635

Closed ykim7263 closed 2 years ago

ykim7263 commented 2 years ago

Dear All,

I was extracting chromatogram information (Rt, intensity) with Chrompeaks function. And when I compared the extracted rt, the intensity of specific m/z with Chrompeaks function, there is some missing intensity information and shown as NA, which was shown as a real data point, when I checked the row data. I have attached some screenshots to help you understand. ss.pptx

Best,

jorainer commented 2 years ago

I'm a little puzzled - you use chrompeaks in the example code (first slide) but then show arginine_ms1_chr which is a XChromatograms that is extracted with the chromatogram function. If I understand you are using the chromatogram function to extract the EIC and in that some of the mass peaks (for rt 41.869 etc) are missing.

Can you please provide the exact call you used to extract the chromatogram (please add that as text directly into the issue and not as a separate file/pptx)? Could be that the m/z range you used for the chromatogram extraction is different to the m/z range you used in the software to look at the raw data.

ykim7263 commented 2 years ago

Sorry, I actually solved the problem, Please close it. Thank you