5 posts
A practical pipeline for normalizing personal proteomics data, from raw intensity matrices through log transformation, method selection, batch correction, and longitudinal re-normalization when new draws arrive.
A working guide to taking raw RNA-seq counts from your own samples through filtering, effective-length correction, TMM or median-of-ratios scaling, and variance stabilization, with the diagnostics that tell you whether the normalization held.
A working guide to turning FASTQ files from your own blood RNA into gene-level expression estimates you can interpret, with the quantification commands, normalization choices, and the failure modes that make people over-read their data.
A working guide to diagnosing and handling batch effects in bulk RNA-seq, from design and TMM normalization through limma, ComBat-seq, and RUV, with the checks that tell you whether the correction helped.
A practical guide to building violin plots from bulk and single-cell RNA-seq counts: which normalization to plot, how to set kernel bandwidth and trimming, and how to read the shapes without fooling yourself.