I cannot get any of the data in a format that the code will read. I have tried some of the various formats at MetaboAnalyst Pro and nothing works without giving errors saying there are sample name issues. I do not know how to format the m/z retention time, polarity, either, as there are no examples. I need help on formatting both the data file and the metadata file to give results, please.
MetabolomicData.csv (80.7 KB)
metadata.csv (6.9 KB)
The parent, medRt and polarity tell you how the compounds were identified by your vendor. These columns are useful for QC and diagnostics, but not for statistical and functional analysis using MetaboAnalyst
MetaboAnalyst requires either compound name/ID (targeted) or peaks (untargeted). In your case, the compound IDs provided by your vendor should be used (i.e. treat the data as targeted). You should remove those columns parent, medRt and polarity, etc.
Your data is mainly for human understanding, you should manually clean them to keep only most informative ones for analysis. See below (note sample names must be the same in both tables)
This is metabolomics data (note we use compound names provided)
This is metadata (note here I assume patient IDs and time points are most important for analysis, you can include other columns such as age, sex, etc)
This topic was automatically closed 12 hours after the last reply. New replies are no longer allowed.
