Olink-NGS
The working directory
~/rds/projects/olink_proteomics/scallop/Olink-NGS
Protein information
Results at work/ are according to the combination of,
- NGS panels – CARDIOMETABOLIC, INFLAMMATION, NEUROLOGY.
- qPCR panels – cvd2, cvd3, inf, neu.
- QC types:
- raw – raw measurements
- QC – NGS QC=PASS
- LOD – set to be NA when < LOD
- col1 – set to NA when 01
for a total of 16 NGS-Olink-QC combinations, with suffexes .dat for correlation and .pdf for scatter plots.
| qPCR panel | Four combinations |
|---|---|
| cvd2 | CARDIOMETABOLIC-cvd2 + [-col1, -LOD, -QC, -raw] |
| cvd3 | CARDIOMETABOLIC-cvd3 + [-col1, -LOD, -QC, -raw] |
| inf | INFLAMMATION-inf + [-col1, -LOD, -QC, -raw] |
| neu | NEUROLOGY-neu + [-col1, -LOD, -QC, -raw] |
The Olink NGS QC=PASS appears to have the highest correlation.
The corresponding density plots are shown in correlogram.pdf.
Genotype-protein association
plink2/ contains genotype-protein association results for MAF>=0.05, INFO>=0.8.
NGS.merge is contained for each of the following p value thresholds,
| Directory | Description | Sentinels | Proteins | cis/trans |
|---|---|---|---|---|
| 1e-5/ | sentinel identification at p=1e-5 | 22,876 | 1,472 | |
| 1e-6/ | sentinel identification at p=1e-6 | 2,788 | 1,241 | |
| 1e-7/ | sentinel identification at p=1e-7 | 561 | 479 | 222/339 |
| 5e-8/ | sentinel identification at p=5e-8 | 427 | 380 | 221/216 |
Note that the following three proteins appear on all four panels and should be treated specifically,
P01375 TNF
P05231 IL6
P10145 CXCL8
see the Venn diagram. 