Hello,
I am planning to conduct a cross-cohort analysis using public metabolomics data obtained from various research papers. Since I did not design and perform the experiments to generate metabolomics data myself, I will not be working with completely raw data but rather starting with data in table format (e.g., concentration or intensity).
I have the following questions:
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When performing statistical analysis (one-factor), there is a distinction between using a concentration table versus a peak intensity table. Does this difference significantly affect the analysis?
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I noticed that the peak intensity table I have contains fewer than 500 peaks, which makes it unsuitable for Mummichog method. As an alternative, I am considering using enrichment and pathway analysis(targeted metabolomics). However, the cohort data I have mostly consists of peak intensity tables, where the columns include metabolite common names. In other words, the format is similar to concentration table, but the values are expressed as intensities. Will this affect the analysis?
Thank you so much for your help.