Computation‎ > ‎

Myeloma Tools

Myeloma GEP Processing-

    This is an automated pipeline that takes in Affymetrix U133Plus2.0 .cel files, processes them with MAS5.0 (using R/bioconductor) and exports out the set of probesets used to calculate many common myeloma gene expression indices.  This version produces files that can be automatically loaded into the "Lab Management Database" solution were the individual indexes are calculated (TC Class, UAMS 70-gene index, Proliferation Index x2 [JJK & PLB], Centrosome Index, Macrophage Index [TC Class version], NFKB Index x2 [JJK & CA])
Future Improvements: Automate index calculations in script skipping the requirement for the database.  Included the SAM/PAM UAMS classifier in the pipeline.
Subpages (1): Myeloma Scripts