Reporting Results

The primary outputs of this pipeline for a given Olink dataset are:

  • A set of interactive HTML reports for pre and post-QC data

  • A yaml file detailing post-QC datasets for carrying forward to analysis

Reports

The HTML reports generated by this pipeline highlight a variety of results:

  1. Principal axes of variation in proteomic differences between individuals

  2. Reports of assays and individuals removed and corresponding QC-criteria missed

  3. ANOVA between axes of proteomic variation and sample-metadata to highlight experimental sources of variation

Here is an example of an interactive report to get a sense of what to expect.

Post-QC Configuration

The pipeline will also deposit a yaml file in results/postqc_yaml/<name>.<date>.postqc.yaml. The entries in this yaml are:

  1. data: the post-QCed data as a TSV.

  2. metadata: the post-QC metadata as a TSV.

  3. pcs: PCs derived from Olink probes.

  4. pcs_sd: Eigenvalues of PCs from proteomic data (e.g. variance explained).

  5. postqc_report: HTML report of postqc data.

  6. preqc_report: HTML report of preqc data.