13 posts
A working guide to hs-CRP, ESR, fibrinogen, ferritin, and IL-6: what each marker tracks, how much of a single value is noise, how to handle samples so cytokine numbers mean something, and where affinity proteomics panels go beyond the standard five.
A glycan age score is a regression of IgG N-glycan peak ratios onto chronological age. Here is what the assay measures, how the number is built, where it is informative, and how to work with the raw peak data yourself.
A plasma proteomics report measures the relative abundance of hundreds to thousands of circulating proteins. Here is what the numbers mean, how the three main platforms differ, and how to analyze your own data without fooling yourself.
A working setup for longitudinal biomarker tracking: a schema that survives lab changes, your own analytical and biological variation estimates, reference change values instead of reference ranges, and trend fitting that does not fire on noise.
A working guide to taking personal proteomics data from raw instrument files or NPX tables to a quantitative matrix, QC'd and normalized, and then to within-person statistics you can defend.
A step-by-step guide to taking a protein abundance matrix, building a defensible ranking statistic, and running over-representation and rank-based enrichment in R, including how to read a negative enrichment score.
A working guide to the Bioconductor DEP and DEP2 packages applied to a single person's mass-spectrometry proteomics: importing MaxQuant or DIA-NN output, handling left-censored missingness, choosing a design that survives n-of-1 sampling, and reading the result table without overclaiming.
A map of the multi-omics vendor market in four layers, what files each layer hands back, and how to evaluate a provider if you want data you can analyze yourself.
A direct look at what a maximal blood panel contains, which assays add real information, where the marketing exceeds the biology, and how to get the raw data in a form you can analyze yourself.
A technical guide to choosing and using a biomarker testing service: what analytes are worth measuring, what the analytical error looks like, how to store and version the results, and where a clinician has to be involved.
Dehydration concentrates plasma by a few percent, which is far too small to explain most ALT and AST elevations. Here is what usually causes them, how to draw a clean measurement, and how to read enzymes against your own genomic and proteomic baseline.
A working pipeline for taking Olink, SomaScan, or DIA-NN output into R: QC, missingness, normalization, and longitudinal within-person modeling of a single individual's plasma proteome.
A technical read of the MPMD/Marek Health blood panel: which assays are chosen well, which markers mislead in trained people, how to control pre-analytic noise, and where a large chemistry panel stops telling you anything new.