Invisible Fence (IF) for Gene Set Analysis (GSA)

We extend the fence method to situations where a true model may not exist or be among the candidate models.  This leads us to a version of the fence called the invisible fence (IF). The gene set analysis (GSA) problem is one which falls under this umbrella. Here one is interested in looking for differential expression patterns of groups or sets of genes often grouped by biological pathways. A unique fast algorithm is developed that scales efficiently and a new limited bootstrap technique derived for carrying out the analysis.

To run a  Gene Set Analysis (GSA), first execute all of the code in the methodIF.R and IF.GSA.R functions. Then run the GSA analysis, use your data with all arguments in the function IF.GSA.

methodIF.R methodIF.R
Size : 1.659 Kb
Type : R
Size : 5.397 Kb
Type : R

Restricted Fence (RF) for Longitudinal Data Analysis

The original fence method can be combined with the idea of restricted maximum likelihood (REML) estimation for model selection with longitudinal data.  A wild bootstrap is developed to adaptively choose the tuning parameter.

To run a Restricted Fence (RF) analysis, you need to execute the codes in methodRF.R only and then use your data with all arguments in methodRF.R (i.e. there is no accompanying function for the RF analysis).

methodRF.R methodRF.R
Size : 5.026 Kb
Type : R

Model Selection with Missing Data

We develop a procedure for model selection in the presence of missing or incomplete data. The E-MS algorithm is in the spirit of the Expectation-Maximization (E-M) algorithm, and treats bot the model and the parameters under the model as quantities for estimation, and to be part of the iterative algorithm. Our procedure is developed under the case that the class of candidate models is finite and includes the E-MS with adaptive fence, and the E-MS with the generalized information criterion (GIC).

Adaptive Fence (AF)

A simplified adaptive fence procedure that reduces the computational burden of the adaptive fence procedure proposed by Jiang et al. [Jiang,J., Rao,J.S., Gu,Z.,Nguyen,T. , 2008.Fence methods for mixed model selection. Ann.Statist. 36,16691692] for mixed model selection problems.The consistency property of the new procedure is established.

To run an Adaptive Fence (AF) analysis, first execute the codes in methodAF.R and fence.lmer.R Then use your data with all arguments in fence.lmer.R.

methodAF.R methodAF.R
Size : 3.796 Kb
Type : R
fence.lmer.R fence.lmer.R
Size : 2.645 Kb
Type : R

Fence Methods for Small Area Estimation (SAE)

The problem of selecting nonparametric models for small area estimation, has recently received much attention. We developed a procedure based on the idea of fence method (Jiang, Rao, Gu and Nguyen 2008) for selecting the mean function for the small areas from a class of approximating splines.

To run a Small area estimation (SAE) analysis, first execute the codes in methodAF.R and fence.lmer.R Then use your data with all arguments in fence.lmer.R.

Size : 2.582 Kb
Type : R