Experimental variance is a major challenge when dealing with high-throughput sequencing data. This variance has several sources: sampling replication, technical replication, variability within biological conditions, and variability between biological conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these c...

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Psycholinguistic data are often analyzed with repeated-measures analyses of variance (ANOVA), but this paper argues that mixed-effects (multilevel) models provide a better alternative method. First, models are discussed in which the two random factors of participants and items are crossed, and not nested. Traditional ANOVAs are compared against these crossed mixed-effects models, for simulated ...

Psycholinguistic data are often analyzed with repeated-measures analyses of variance (ANOVA), but this paper argues that mixed-effects (multilevel) models provide a better alternative method. First, models are discussed in which the two random factors of participants and items are crossed, and not nested. Traditional ANOVAs are compared against these crossed mixed-effects models, for simulated ...

Inference for variance components in linear mixed models of ANOVA type, including estimation and testing, has been investigated when the number of fixed effects is fixed. However, for high-dimensional data, this number is large and would be regarded as a divergent value as the sample size goes to infinity. In this paper, existing tests are extended to handle this problem with a sparse model str...

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii DEDICATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv LIST OF TABLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi

ANOVA provides a general approach to the analysis of single and multiple factor experiments on both one- and two-color microarray platforms. Mixed model ANOVA is important because in many microarray experiments there are multiple sources of variation that must be taken into consideration when constructing tests for differential expression of a gene. The genome is large, and the signals of expre...

32.1 Smoothed ANOVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586 32.1.1 Zhang et al.’s SANOVA proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586 32.1.2 Maŕi-Dell’Olmo et al.’s SANOVA proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . 588 32.2 Some Specific Application...