How does Mass Dynamics treat experiment outliers?

For clarity, outliers are considered as runs that are:

These outliers:

Will not be included in the statistical analysis.
- Effects of this:
  - Samples will not be included in any differential expression analysis (pairwise comparison or ANOVA table or future ones)
  - No protein will be declared as significant based on the intensity values in those samples.
Will still be present in the intensity table.
- Effects of this:
  - Will appear in the QC report
  - Can appear in the Heatmap if the user does not exclude them
  - Will appear in the violin/dot plots

Reasons for keeping these outliers in these plots are:

- Most raw data processing software will perform steps that include (amongst others) normalisation, identification, match between runs, etc. these processes are dependent on which files/runs are included in the raw data processing steps and, as such, should be reflected in the QC report.
- The giant QC report document will always include those samples for reproducibility, record and accountability of how the processing was done.

At present, and where possible, our recommendation for any outliers would be to consider removing them prior to the raw data processing.