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:
Principal axes of variation in proteomic differences between individuals
Reports of assays and individuals removed and corresponding QC-criteria missed
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:
data: the post-QCed data as a TSV.
metadata: the post-QC metadata as a TSV.
pcs: PCs derived from Olink probes.
pcs_sd: Eigenvalues of PCs from proteomic data (e.g. variance explained).
postqc_report: HTML report of postqc data.
preqc_report: HTML report of preqc data.