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Empirical threshold values for quantitative trait mapping.
An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand, and is demonstrated using two real data sets derived from F(2) and recombinant inbred plant populations. Expand
R/qtl: QTL Mapping in Experimental Crosses
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two- QTL genome scans by multiple methods. Expand
Permutation tests for multiple loci affecting a quantitative character.
Two extensions of the permutation-based method for estimating empirical threshold values are presented, which yield critical values that can be used to construct tests for the presence of minor QTL effects while accounting for effects of known major QTL. Expand
Optimizing parental selection for genetic linkage maps.
The objectives of this research were to calculate polymorphism information content values of 51 low-copy DNA clones and use the resulting values to choose potential mapping parents and to identify Genotype pairs that would map more highly informative DNA clones compared with a population derived from the most polymorphic potential parents. Expand
Analysis of Variance for Gene Expression Microarray Data
It is demonstrated that ANOVA methods can be used to normalize microarray data and provide estimates of changes in gene expression that are corrected for potential confounding effects and establishes a framework for the general analysis and interpretation of micro array data. Expand
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
Although no single mouse model recapitulated all the expression features of a given human subtype, these shared expression features provide a common framework for an improved integration of murine mammary tumor models with human breast tumors. Expand
A Hidden Markov Model approach to variation among sites in rate of evolution.
The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences and it is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogenies what assignment of rates to sites has the largest posterior probability. Expand
Statistical tests for differential expression in cDNA microarray experiments
Analysis of variance (ANOVA) can be used, and the mixed ANOVA model is a general and powerful approach for microarray experiments with multiple factors and/or several sources of variation. Expand
Fundamentals of experimental design for cDNA microarrays
Fundamental issues of how to design an experiment to ensure that the resulting data are amenable to statistical analysis are discussed. Expand
Experimental design for gene expression microarrays.
We examine experimental design issues arising with gene expression microarray technology. Microarray experiments have multiple sources of variation, and experimental plans should ensure that effectsExpand