Running DEP on Your Own Plasma Proteomics Data
A working guide to the Bioconductor DEP and DEP2 packages for one person's mass-spectrometry proteomics. Covers import, missing values and design.
Tag: limma
3 posts
How to Correct Batch Effects in Your Own RNA-Seq 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.
How to Analyze Your Own Plasma Proteomics Data in R
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.