Differential Expression Analysis Plan

[ ] PCA plot on normalized within study data with all technical covariates annotated
[ ] DESeq2 on count data for 2 conditions studies
[ ] Voom + limma on count data for 2 condtion studies
[ ] Voom + linma + linear mixed model for >2 condition temporal studies
[ ] Minimum set of adjustments in single model analysis (If available): RIN, Age, Batch, Gender*
[ ] Push all analysis results to synapse with appropriate annotations/provenance

@RamiOran will design python wrapper for these analyses @blogsdon to deploy PCA/batch code

Sage-Bionetworks / BaylorSage