This repository includes the source code for the analyses I presented at the EDEN sponsored symposium "Understanding First Order Phenotypes: Transcriptomics for Emerging Model Systems" at the 2013 SICB conference, described in abstract S4-2.1.

This study is a collaborative project by Brown University faculty members:

All collaborators contributed to the code presented here.

Additional details will be provided in a forthcoming publication. A preprint of this publication is available at:

Dunn, CW, X Luo, and Z Wu (2013) Phylogenetic analysis of gene expression. arXiv:1302.2978

Many thanks to Joe Felsenstein for helpful discussions about multivariate comparative analyses.


To run the simulation and analyses, execute the following shell command:

R CMD BATCH simulation.r

This will regenerate the pdf file.


This code implements the two regularization methods described in:

Bickel, P. J. & Levina, E. Covariance regularization by thresholding. Ann. Statist. 36, 2577–2604 (2008). doi:10.1214/08-AOS600

Luo, X. High Dimensional Low Rank and Sparse Covariance Matrix Estimation via Convex Minimization. arXiv.org (2011). arxiv


This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.