Search

Background High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously. The utility of a plot, in turn, is contingent on both its interpretability and its efficiency. Results The shivplot, a graphical technique motivated by microarrays but applicable to any replicated high-throughput data set, is described. The plot capitalizes on the strengths of three well-established plotting graphics – a boxplot, a distribution density plot, and a variability vs intensity plot – by effectively combining them into a single representation. Conclusion The utility of the new display is illustrated with microarray data sets. The proposed graph, retaining all the information of its precursors, conserves space and minimizes redundancy, but also highlights features of the data that would be difficult to appreciate from the individual display components. We recommend the use of the shivplot both for exploratory data analysis and for the communication of experimental data in publications.

Background DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with data publicly available for mining by other investigators. Under most circumstances, validation of differential expression of genes is performed on a gene to gene basis. Thus, it is not possible to generalize validation results to the remaining majority of non-validated genes or to evaluate the overall quality of these studies. Results We present an approach for the global validation of DNA microarray experiments that will allow researchers to evaluate the general quality of their experiment and to extrapolate validation results of a subset of genes to the remaining non-validated genes. We illustrate why the popular strategy of selecting only the most differentially expressed genes for validation generally fails as a global validation strategy and propose random-stratified sampling as a better gene selection method. We also illustrate shortcomings of often-used validation indices such as overlap of significant effects and the correlation coefficient and recommend the concordance correlation coefficient (CCC) as an alternative. Conclusion We provide recommendations that will enhance validity checks of microarray experiments while minimizing the need to run a large number of labour-intensive individual validation assays.

Gene expression arrays present unique challenges for statistical inference. The typically small number of replicated expression values in array studies make the use of standard parametric statistical tests problematic. Such tests have low sensitivity and return potentially inaccurate probability values. This paper describes novel alternative statistical modeling procedures which circumvent these difficulties by pooling random error estimates obtained from replicate expression values. The procedures, which can be used with both micro- and macro-arrays, include outlier detection, confidence intervals, statistical tests of differences between conditions, and statistical power analysis for determining number of replicates needed to detect between-condition differences of specified magnitude. The methods are illustrated with experimental data.

Jain et al. introduced the Local Pooled Error (LPE) statistical test designed for use with small sample size microarray gene-expression data. Based on an asymptotic proof, the test multiplicatively adjusts the standard error for a test of differences between two classes of observations by π/2 due to the use of medians rather than means as measures of central tendency. The adjustment is upwardly biased at small sample sizes, however, producing fewer than expected small P-values with a consequent loss of statistical power. We present an empirical correction to the adjustment factor which removes the bias and produces theoretically expected P-values when distributional assumptions are met. Our adjusted LPE measure should prove useful to ongoing methodological studies designed to improve the LPE's; performance for microarray and proteomics applications and for future work for other high-throughput biotechnologies. Availability: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org). Contact: robert.nadon@mcgill.ca

Motivation: High-throughput screening (HTS) plays a central role in modern drug discovery, allowing for testing of >100 000 compounds per screen. The aim of our work was to develop and implement methods for minimizing the impact of systematic error in the analysis of HTS data. To the best of our knowledge, two new data correction methods included in HTS-Corrector are not available in any existing commercial software or freeware. Results: This paper describes HTS-Corrector, a software application for the analysis of HTS data, detection and visualization of systematic error, and corresponding correction of HTS signals. Three new methods for the statistical analysis and correction of raw HTS data are included in HTS-Corrector: background evaluation, well correction and hit-sigma distribution procedures intended to minimize the impact of systematic errors. We discuss the main features of HTS-Corrector and demonstrate the benefits of the algorithms. Availability: The Microsoft Windows version and a detailed description of the software are freely available at the following URL: Contact: makarenkov.vladimir@uqam.ca

We argue that both nomothetic and idiographic research strategies can advance scientific knowledge of therapeutic hypnosis. In particular, practitioners can make idiographic contributions to the scientific literature in a manner that will be received positively by a growing number of behavioral scientists. Broad methodological issues and concerns specific to hypnosis research are discussed.

We sought to extend the finding (LaurencePerry, 1983) that it is possible through hypnosis to create a pseudomemory of a specific event. Subjects were compared on their responses to a hypnotic suggestion. We also examined the relation between nonhypnotic measures (Preference for an Imagic Cognitive Style [PICS] test and the Tellegen Absorption Scale [TAS]) and response to the suggestion. Highly (45.45%) and moderately-highly (46.15%) susceptible subjects believed that the pseudomemory was veridical, but none of the low susceptible subjects did so. Together, hypnotic susceptibility, the PICS, and their interaction more strongly predicted pseudomemory creation than any of these main effects alone. Performance on the TAS was also related to the occurrence of pseudomemory, but this relation was redundant with performance on the other measures. These results point to the complexity of the variables involved in pseudomemory creation during hypnosis.

The empirical work relating hypnotizability, the hypnotic situation, and the reports of hypnotic depth is reviewed and evaluated. Asking Ss to assess their hypnotic depth is a complex task involving the interaction of experiential, cognitive, and contextual variables. Accordingly, future experimental work should take into account this multidimensionality; phenomenological, situational, cognitive, and motivational factors implicated in verbal reports should be explored in terms of their respective relationships with both hypnotizability and self-ratings of hypnotic depth. More sophistication in the experimental inquiries of hypnotic depth is required in order to fiirther our understanding of the cognitive and affective structures underlying the hypnotic experience.

The present paper reports an initial attempt to create a pseudomemory in a group of highly hypnotizable individuals. It was found that for approximately 50% of Ss tested, recall of a specific event was modified when Ss integrated hypnotically suggested inaterial which then posthypnotically was believed to be veridical. This modification in a previously reported memory was linked to a particular cognitive style found in high hypnotizalde Ss, namely dual cognitive functioning. Ss reporting duality in hypnotic age regression, and, to a lesser extent, the hidden observer effect, were found to be the most prone to accept a suggested memory as real. These findings suggest the need to emphasize the importance of a cognitive-phenomenological approach to hypnosis and hypnotizability.

In this article, we report two experiments in which various measures thought to be related to hypnotizability were analyzed by stepwise discriminant analysis techniques. Absorption (Tellegen, 1981, 1982; Tellegen & Atkinson, 1974) and preference for an imagic style of thinking (Isaacs, 1982) were robust predictors of hypnotizability; each variable accounted for significant variance in hypnotizability at their respective steps in two samples and correctly classified a significant proportion of low- and high-hypnotizable subjects in the discriminant analyses. The addition of two other variables in Experiment 2--a Sleep-Dream score derived from Evans's (1977) Cognitive Control of Sleep Mentation subscale and Gibson's (1985) Dream Questionnaire, and the Belief in the Supernatural subscale of the Taft (1969) Experience Questionnaire--increased the correct classification of the medium-hypnotizable subjects from chance levels to 74%. It is argued that a confirmatory and hierarchical approach is needed in future studies to explore correlates of hypnotizability more fully.

The present study sought to explore potential response differences to a suggestion for posthypnotic amnesia between those high hypnotizable Ss who do and those who do not manifest the hidden observer effect. In line with the hypothesis that Ss who responded to the hidden observer suggestion are more highly engaged in cognitive monitoring of their experience and behavior (Nogrady, McConkey, Laurence, & Perry, 1983), it was predicted that these Ss would recall more Stanford Hypnotic Susceptibility Scale, Form C (Weitzenhoffer & Hilgard, 1962) hypnotic items, and in greater detail, following the reversal of amnesia than would their no-hidden observer counterparts. In this regard, both the quantity and the quality of posthypnotic recall was examined in 15 high, 11 high-medium, and 11 low hypnotizable Ss. Data on posthypnotic recall from low and high-medium hypnotizable Ss revealed the comparability of the present sample to samples of other studies that have investigated posthypnotic recall using stan...

The revised form of the Absorption Scale extracted from Tellegen's Multidimensional Personality Questionnaire (Tellegen, 1981; Tellegen & Atkinson, 1974) and the Short Imaginal Processes Inventory (Huba, Aneshensel, & Singer, 1981), a self-report questionnaire concerned with daydreaming activity, were administered to 2 samples of Ss (N = 479, N = 476), who also received the Harvard Group Scale of Hypnotic Susceptibility, Form A (Shor & E. Orne, 1962). In both samples, hypnotizability was significantly correlated with absorption (average r = .24) and with a subscale measuring positive-constructive daydreaming (average r = .13). Absorption and positive-constructive daydreaming were also highly correlated (average r = .57). Of the subscales of the positive-constructive daydreaming scale, only those relating to positive reactions to daydreaming, and problem solving in daydreaming, consistently correlated with hypnotizability. Daydreaming and absorption each share some features in common with hypnosis, but they appear to have more in common with each other.