An increasingly popular tool for nonparametric smoothing are penalized splines (P-splines) which use low-rank spline bases to make computations tractable while maintaining accuracy as good as smoothing splines. This paper extends penalized spline methodology by both modeling the variance...

Time series models relating short-term changes in air pollution levels to daily mortality counts typically assume that the effects of air pollution on the log relative rate of mortality do not vary with time. However, these short-term effects might plausibly vary by season. Changes in the...

Microsatellite instability (MSI) testing is a common screening procedure used to identify families that may harbor mutations of a mismatch repair gene and therefore may be at high risk for hereditary colorectal cancer. A reliable estimate of sensitivity and specificity of MSI for detecting...

Penalized splines can be viewed as BLUPs in a mixed model framework, which allows the use of mixed model software for smoothing. Thus, software originally developed for Bayesian analysis of mixed models can be used for penalized spline regression. Bayesian inference for nonparametric models...

High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing step. Statistical...

This paper describes the use of model-based geostatistics for choosing the optimal set of sampling locations, collectively called the design, for a geostatistical analysis. Two types of design situations are considered. These are retrospective design, which concerns the addition of sampling...

Background: The analysis and interpretation of change in cognitive function test scores after Coronary Artery Bypass Grafting (CABG). Longitudinal studies with multiple outcomes present considerable statistical challenges. Application of hierarchical linear statistical models can estimate the...

Complementary DNA (cDNA) microarrays are a powerful tool for genomic analysis, but have noise components that make inferences regarding gene expression inefficient and potentially misleading. Background fluorescence, whether attributable to non-specific binding or other sources, is an important...

Cross-study validation of gene expression investigations is critical in genomic analysis. We developed an R package and associated object definitions to merge and visualize multiple gene expression datasets. Our merging functions use arbitrary character IDs and generate objects that can...

Over 10% of the data sets catalogued in the Gene Expression Omnibus Database involve messenger RNA samples that have been pooled prior to hybridization. Pooling affects data quality and inference, but the exact effects are not yet known as pooling has not been systematically studied in the...