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Intensity of compund in each group in annotated_MS_peaks-cleaned.csv is far from that in raw data #9

Closed g0079 closed 2 years ago

g0079 commented 2 years ago

Hi, I'am using MS-CleanR to deal with metabonnomics data. It's very convenient to do data clean after MS-DIAL data processing. But I found that the intensity of compund in each group in annotated_MS_peaks-cleaned.csv is far different from that in raw data, for example, the intensity in Height_xxx.txt exported from MS-DIAL. I would like to know what kind of operations was implemented by ms-cleanR to the raw intensity, and whether there is a way to keep the raw intensity in the output of ms-cleanR. Thank you very much.

guikool commented 2 years ago

Dear user, Tow files are generated after MSCleanR data processing: annotated_MS_peaks_normalized: the normalization is done according to "sum area" of each feature. Meaning that each sample will have an identical total sum area -->suitable for further statistical analysis annotated_MS_peaks_cleaned: Correspond to integration done by MS-Dial: suitable to apply your own normalization process (in metaboanalyst for instance)

g0079 commented 2 years ago

Now I,m sure no log transformation was applied on the raw data, Thank you!