Daniel W. Schafer

Learn More
GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments,(More)
The objectives were to determine if strategic supplementation of range cows with a long-acting (6 mo), trace mineral, reticulorumen bolus containing Cu, Se, and Co would: (1) increase cow BCS and BW, and calf birth, weaning, and postweaning weights, or weight per day of age (WDA); (2) increase liver concentrations of Cu or Zn in cows, or blood Se, Cu, or Zn(More)
This paper presents an EM algorithm for semiparametric likelihood analysis of linear, generalized linear, and nonlinear regression models with measurement errors in explanatory variables. A structural model is used in which probability distributions are specified for (a) the response and (b) the measurement error. A distribution is also assumed for the true(More)
Statistical dose-response analyses in radiation epidemiology can produce misleading results if they fail to account for radiation dose uncertainties. While dosimetries may differ substantially depending on the ways in which the subjects were exposed, the statistical problems typically involve a predominantly linear dose-response curve, multiple sources of(More)
Exposure assessment poses special problems in air pollution epidemiology. This paper proposes a probit regression model for binary and ordinal outcomes that uses exposure validation information to develop estimates for the coefficient of the true exposure when only the inaccurate 'surrogate' measure of exposure is available for the individuals in the health(More)
In the 1940s and 1950s, children in Israel were treated for tinea capitis by irradiation to the scalp to induce epilation. Follow-up studies of these patients and of other radiation- exposed populations show an increased risk of malignant and benign thyroid tumors. Those analyses, however, assume that thyroid dose for individuals is estimated precisely(More)
This article demonstrates semiparametric maximum likelihood estimation of a nonlinear growth model for fish lengths using imprecisely measured ages. Data on the species corvina reina, found in the Gulf of Nicoya, Costa Rica, consist of lengths and imprecise ages for 168 fish and precise ages for a subset of 16 fish. The statistical problem may therefore be(More)
RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and(More)
We consider the analysis of longitudinal ordinal data, meaning regression-like analysis when the response variable is categorical with ordered categories, and is measured repeatedly over time (or space) on the experimental or sampling units. Particular attention is given to the multivariate ordinal probit regression model, in which the correlation between(More)
This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing(More)