Croteau-Chonka, D.C. and Raby, B.A. (2018) [https://doi.org/10.1164/rccm.201709-1964LE]

• Run code/data/make_hthgu133pluspm_db.R, which will create the custom annotation package you will then need to install to be able to process the U-BIOPRED GEO data (GSE69683).

• Run code/run_analysis.R, which will run the following scripts:

  • code/data/create_ubiopred_eset.R, which will generate a processed ExpressionSet with gene expression principal components and estimated blood cell counts.

  • code/models/run_gsea.R, which will run the differential gene expression (DGE) analysis and then the gene set enrichment analysis (GSEA).

  • code/visualization/figure01.R, which will make a summary figure for the primary GSEA results and provide other additional analysis details.

  • code/visualization/table01.R, which will make a summary table describing the characteristics of the U-BIOPRED study cohort.

The data objects the from analysis environment will end up in the data/final/ directory and the summary figure and other analysis output will end up in the reports/publication/ directory.