This is the vignette of the Bioconductor compliant packege stam. We describe our implementation of structured analysis of microarray data for decomposing complex clinical phenotypes in clinical gene expression profiling studies. Corresponding author: [email protected]

OBJECTIVE To assess the extent to which different forms of summarising diagnostic test information influence general practitioners' ability to estimate disease probabilities. DESIGN Controlled questionnaire study. SETTING Three Swiss conferences in continuous medical education. PARTICIPANTS 263 general practitioners. INTERVENTION Questionnaire with multiple choice questions about terms ...

OBJECTIVE A significant portion of police work involves contact with persons who have mental illness. This study examined how knowledge that a person has a mental illness influences police officers' perceptions, attitudes, and responses. METHODS A total of 382 police officers who were taking a variety of in-service training courses were randomly assigned one of eight hypothetical vignettes de...

By combining the false belief (FB) and photo (PH) vignettes to identify theory-of-mind areas with the false sign (FS) vignettes, we re-establish the functional asymmetry between the left and right temporo-parietal junction (TPJ). The right TPJ (TPJ-R) is specially sensitive to processing belief information, whereas the left TPJ (TPJ-L) is equally responsible for FBs as well as FSs. Measuring BO...

This vignette provides examples of how to use the package FEM to identify interactome hotspots of differential promoter methylation and differential expression, where an inverse association between promoter methylation and gene expression is assumed [1]. By “interactome hotspot” we mean a connected subnetwork of the protein interaction network (PIN) with an exceptionally large average edge-weig...

Data from self-report tools cannot be readily compared between cultures due to culturally specific ways of using a response scale. As such, anchoring vignettes have been proposed as a suitable methodology for correcting against this difference. We developed anchoring vignettes for the Big Five Inventory-44 (BFI-44) to supplement its Likert-type response options. Based on two samples (Rwanda: n ...

OBJECTIVES Contrary to lay theories, past work does not suggest robust age differences in wisdom-related knowledge across the adult life span. This study investigated a potential moderator of age differences in wisdom-related knowledge: The age relevance of a given wisdom task. METHOD To test this moderator, 192 participants covering the adult life span were asked to think aloud about a tradi...

This vignette tests the Markov chain Monte Carlo (MCMC) implementation of Rpackage FME (Soetaert and Petzoldt 2010). It includes the delayed rejection and adaptive Metropolis algorithm (Haario, Laine, Mira, and Saksman 2006)

This study examined the psychometric properties of performance measures for three novel, interactive virtual reality vignette exercises developed to assess social competency skills of at-risk adolescents. Performance data were collected from 117 African-American male 15-17 year olds. Data for 18 performance measures were obtained, based on adolescents' interaction with a provocative virtual tee...

This lab will walk you through an end-to-end RNA-Seq differential expression workflow. We will start from the FASTQ files, align to the reference genome, prepare gene expression values as a count table by counting the sequenced fragments, perform differential gene expression analysis, and visually explore the results. This lab covers the basic introduction. For a more in-depth explanation of th...