Chapter 3 Manual
Important features and technical details are described in this chapter.
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3.2 Harmonization details
The names of metabolites from each cohort has been mapped or harmonized to a common name. This important stage facilitates comparison of metabolites across different studies that use different platforms and/or naming conventions.
3.3 Security and Privacy
3.4 Integrity checks
Prior to running the models for analyses, CA conducts multi-level checks to ensure data and models are appropriate for analyses.
The following conditions are checked:
- Missing Subject ID or Metabolite ID in the VarMap sheet
- Subject ID or Metabolite ID provided in VarMap sheet do not correspond to a column in Metabolites and SubjectData sheets, respectively
- Metabolites IDs in Metabolites and SubjectMetabolites sheets do not match
- Subject IDs in SubjectData and SubjectMetabolites sheets do not match
If any of the following conditions failed, the analyses will be suspended and corrections to the data are required. The data integrity checks will also flag the following but will proceed with the analyses:
- Number of subjects in SubjectData and SubjectMetabolites sheets do not match
- Metabolite abundances from SubjectMetabolites contains duplicate columns (metabolites) or rows (subjects)
- There are duplicate subject IDs in the subject information SubjectData sheet
- There are duplicate metabolite IDs in the metabolite information Metabolites sheet
Models are also validated using the CARET package to check for the following conditions:
- Variables with zero variance.
- Highly correlated covariates.