Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments

A two-groups mixed-effects model for the comparison of (normalized) microarray data from two treatment groups is considered. Most competing parametric methods that have appeared in the literature are obtained as special cases or by minor modification of the proposed model. Approximate maximum likelihood fitting is accomplished via a fast and scalable algorithm, which we call LEMMA (Laplace approximated EM Microarray Analysis). The posterior odds of treatment $\times$ gene interactions, derived from the model, involve shrinkage estimates of both the interactions and of the gene specific error variances. Genes are classified as being associated with treatment based on the posterior odds and the local false discovery rate (f.d.r.) with a fixed cutoff. Our model-based approach also allows one to declare the non-null status of a gene by controlling the false discovery rate (FDR). It is shown in a detailed simulation study that the approach outperforms well-known competitors. We also apply the proposed methodology to two previously analyzed microarray examples. Extensions of the proposed method to paired treatments and multiple treatments are also discussed.Comment: Published in at http://dx.doi.org/10.1214/10-STS339 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Understanding the Computational Requirements of Virtualized Baseband Units using a Programmable Cloud Radio Access Network Testbed

Cloud Radio Access Network (C-RAN) is emerging as a transformative architecture for the next generation of mobile cellular networks. In C-RAN, the Baseband Unit (BBU) is decoupled from the Base Station (BS) and consolidated in a centralized processing center. While the potential benefits of C-RAN have been studied extensively from the theoretical perspective, there are only a few works that address the system implementation issues and characterize the computational requirements of the virtualized BBU. In this paper, a programmable C-RAN testbed is presented where the BBU is virtualized using the OpenAirInterface (OAI) software platform, and the eNodeB and User Equipment (UEs) are implemented using USRP boards. Extensive experiments have been performed in a FDD downlink LTE emulation system to characterize the performance and computing resource consumption of the BBU under various conditions. It is shown that the processing time and CPU utilization of the BBU increase with the channel resources and with the Modulation and Coding Scheme (MCS) index, and that the CPU utilization percentage can be well approximated as a linear increasing function of the maximum downlink data rate. These results provide real-world insights into the characteristics of the BBU in terms of computing resource and power consumption, which may serve as inputs for the design of efficient resource-provisioning and allocation strategies in C-RAN systems.Comment: In Proceedings of the IEEE International Conference on Autonomic Computing (ICAC), July 201

Bayesian testing of many hypotheses ×\times many genes: A study of sleep apnea

Substantial statistical research has recently been devoted to the analysis of large-scale microarray experiments which provide a measure of the simultaneous expression of thousands of genes in a particular condition. A typical goal is the comparison of gene expression between two conditions (e.g., diseased vs. nondiseased) to detect genes which show differential expression. Classical hypothesis testing procedures have been applied to this problem and more recent work has employed sophisticated models that allow for the sharing of information across genes. However, many recent gene expression studies have an experimental design with several conditions that requires an even more involved hypothesis testing approach. In this paper, we use a hierarchical Bayesian model to address the situation where there are many hypotheses that must be simultaneously tested for each gene. In addition to having many hypotheses within each gene, our analysis also addresses the more typical multiple comparison issue of testing many genes simultaneously. We illustrate our approach with an application to a study of genes involved in obstructive sleep apnea in humans.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS241 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org