statistical data interpretation

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..With a focus on prediction assessment, we compare several methods for estimating the 'true' prediction error of a prediction model in the presence of feature selection...

..In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies...

..It complements an earlier work by O'Hagan et al. (Pharmaceutical Statistics 2005; 4:187-201) published in this journal. Computer codes to calculate the average success probability are included...

..The proposed extensions to the VPC are illustrated by a pharmacokinetic simulation example and applied to a pharmacodynamic disease progression example...

..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities...

..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...

..Affinity propagation found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time...

..The method is implemented in a software package called Icasso...

..Additionally, this article offers some technical considerations and information on statistical analysis of real-time PCR data...

..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...

..Studies should be designed with reference to the overall distribution of ICCs and with attention to features that increase efficiency...

..This review discusses those determinants, presents a checklist for clinicians, and makes recommendations for greater consideration of external validity in the design and reporting of RCTs...

..The aim of this study is to define and illustrate metrics for the external evaluation of a population model...

..Given an observed test statistic and its degrees of freedom, one may compute the observed P value with most statistical packages. It is unknown to what extent test statistics and P values are congruent in published medical papers...

..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...

..We propose a simple method to approximate a risk ratio from the adjusted odds ratio and derive an estimate of an association or treatment effect that better represents the true relative risk...

..Finally, a statistical framework for assessing the reliability of obtained HGTs by bootstrap analysis is also presented...

..We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas...

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..DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/...

..It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription...

..There is a need for critical review of the statistical analysis and reporting in published microarray studies that focus on cancer-related clinical outcomes...

..AVAILABILITY: The software is implemented in the R language, is open source and available for download free of charge through the Bioconductor (http://www.bioconductor.org) project...

..In this essay, I discuss the implications of these problems for the conduct and interpretation of research...

..The paper does not claim to be definitive; it purports to act as a guide for those researchers who wish to exploit the Delphi methodology...

..The second part of the paper summarizes results of a study of the size and power of two-part models. It proposes that two-part models are a useful alternative to the t-test and the Wilcoxon test...

..The software package GOSSIP implements our method and is made freely available at http://gossip.gene-groups.net/...

..In many situations, estimates of linear combinations are invariant with respect to covariance structure, yet standard errors of the estimates may still depend on the covariance structure...

..It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context...

..The results show the utility of the I(2) index as a complement to the Q test, although it has the same problems of power with a small number of studies...

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..The above asymmetries were observed in men and women. Our results thus provide confirmation of the known structural asymmetries in the human brain as well as new findings that may stimulate further research of hemispheric specialization...

..In this article, we present Meta-DiSc, a Windows-based, user-friendly, freely available (for academic use) software that we have developed, piloted, and validated to perform diagnostic meta-analysis...

..We demonstrate this approach by accurate SNP predictions in human ESTs aligned to finished and working-draft quality genomic sequences, a data set representative of the typical challenges of sequence-based SNP discovery...

..This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species...

..In addition, the serious pitfalls of using more traditional methods based on parameters in logistic regression models are illustrated...

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..Methodological issues regarding estimation of complex ML-SEMs and the evaluation of model fit are discussed. Further potential applications of ML-SEMs are explored...

..Studies of diagnostic accuracy most often report pairs of sensitivity and specificity. We demonstrate the advantage of using bivariate meta-regression models to analyze such data...

..In those cases, the two-part models are not far behind, although statistically significantly poorer with respect to power. Published in 2001 by John Wiley & Sons, Ltd...

..The motor memory trace in rats may require changes in motor cortex organization other than those detected by stimulation mapping...

..We have evaluated the validity of using the CV error estimate of the optimized classifier as an estimate of the true error expected on independent data...

..Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data...

..Simulation results of the robustness of these two tests indicate that the more computationally involved MAX test is preferable...

..Furthermore, some have advocated for the use of regression adjustment to estimate the effect of treatment after adjusting for potential imbalances in prognostically important baseline covariates between treatment groups...

..The results from our simulation study showed that, for missing data patterns that are relevant to the Pathways study, this procedure has high power and maintains the type I error rate. Published in 2001 by John Wiley & Sons, Ltd...

..In case of multiple significance tests a note on the error rate that will be controlled for is desirable...

..A brief outlook of the application of such approaches to the newest microarray-based technologies (Chromatin-ImmunoPrecipitation, ChIP-on-chip) concludes the review...

..The results of the analysis are presented as a set of HTML pages. Additionally, all values and plots are available as either text files or pdf and png files. AVAILABILITY: http://bioconductor.org/..

..This ability, similar to semantic polysemy in text, provides a general method for robust molecular pattern discovery...

..The methods presented in this paper can be used by applied researchers to protect against loss of power, or to choose a design which reduces the impact of uncertainty in the ICC...

..Methods are illustrated on data from the Women Take Pride study, an assessment of behavioral treatments for women with heart disease...

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..In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data...

..This paper highlights some of the distinct ways in which outcome based subgroup analysis occurs, describes the hazards associated with it, and proposes a simple alternative approach to counter its analytic bias...

..The fact that counts are not being recorded during periods in which the monitor is not worn means that many common estimators of daily physical activity are biased downward...

..The authors studied the effect of desflurane on resting and visual evoked unit activity in rat visual cortex in vivo...

..We apply our methods to a fMRI data set, demonstrating their ability to localize subtle artifacts and to discover systematic experimental variation not captured by the model...

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..In this spirit, I seek to assess the performance of classifiers simpler than even PAM...

..As case studies, we present parametric maps of lesions in patients suffering from stroke and glioblastoma at different stages of evolution...

..Our experience suggests that association mining may also be useful for selection of variables prior to using logistic regression...

..We show examples of simulation and in vivo reconstructed data which demonstrate the potential of the statistical approach...

..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...

..AVAILABILITY: Libraries of S-plus and R routines to implement the method are freely available from www.stjuderesearch.org/depts/biostats...

..By contrast, Expresso can use either IIV data or median intensity values (MIV). Here, we compare Expresso and TM4 analysis of two experiments and assess the results against qRT-PCR data...

..It has been shown that our proposed method has a better control of the FDRs and a higher power than the standard permutation method to detect differentially expressed genes because of the better approximated tail probabilities...

..genopole.cnrs.fr/spatt) implementing all these methods is then used to compare all these approaches in terms of computational time and reliability in the most complete pattern statistics benchmark available at the present time...

..g. sequence analysis, etc.). AVAILABILITY: Our algorithm is available on request from the authors and soon to be posted on the web. See author's homepage for details, http://www.seas.ucla.edu/~liaoj/..

..An illustrative example from a cancer study is provided...

..Experiments demonstrate a high rates of convergence on complex scenes with varying degrees of overlap...

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..Here, we consider a novel approach that uses the variability between arrays to provide an extra source of information that can enhance gene expression analyses...

..We also examine the impact on required sample size when adding an extra heterogeneous population to a study...

..The methodology is applied to a motivating study of patients with psoriatic arthritis in which the events of interest are the onset of joint damage according to 2 different criteria...

..In order to properly estimate biological effects, these biases must be identified and discarded...

..The approach allows outcomes and covariates to be missing at either of the two levels, and the HLM of interest can involve the regression of any subset of variables on a disjoint subset of variables conceived as covariates...

..These new methods are compared with existing approaches by simulation. The National Health and Nutrition Examination Survey data are used to illustrate these approaches...

..The relationship and relative performance of these methods in two-sample comparisons is currently unknown...

..The discussion in this paper is illustrated by a hypothetical example, which nevertheless resembles the findings from a confirmatory trial involving the evaluation of a biologic for severe sepsis...

..The contaminated site exhibited significant short-range spatial variability in elemental composition, which resulted in sampling uncertainties of 20-30%...

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..In addition, it is not clear which method is more suitable for the unbalanced data...

..Both methods provide unbiased estimates when the missingness mechanism is missing at random (MAR) assumption. Sensitivity analyses have been performed for cases when the MAR assumption is in question...

..We identify a number of amino acid pairs that exhibit either strong or weak association...

..Using simulated data, we also show pitfalls in drawing statistical inference when the within-subject correlation in longitudinal gene expression data is ignored...

..Hence, the computational methods should preferably be robust against such anomalies in the data...

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..This paper examines feature selection techniques for proteomic mass spectrometry...

..However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs)...

..Similarly, irrelevant gene combinations can be discovered in the case of gene expression based classification...

..In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis...

..A similar situation occurs when DNA methylation data are investigated. In that case, there are null values (undetectable methylation) and observed positive values. For these data, we propose a two-part permutation test...

..Therefore, we briefly discuss the roles of experimental design, data screening, normalization, and statistical diagnostics when evaluating ELISA microarray concentration estimation errors...

..In summary, this Core will provide the bioinformatics that will be crucial to the success of Projects 2 and 3, and will provide statistical support in terms of experimental design and data analysis for all Consortium members...

..Eventually, optimal exercise regimens will be sought for both primary and secondary prevention of OA at various joints and stages. ..

..Targeting PiHDL with interventions that restore protective function to HDL might be considered for prevention of ATH in both lupus and non lupus patients. ..

..This integrated research program is intended to: 1) improve the presymptomatic diagnosis and treatment of LQTS; and 2) provide a fundamental understanding of the molecular basis of repolarization-related cardiac arrhythmias. ..

..The new knowledge will have significant impact on prevention or treatment of AD. ..

..Finally, Dr. Stein will determine if these medications impair postprandial clearance of triglyceride-containing lipoproteins by assessing lipid and lipoprotein responses to an oral fat load. ..

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..Identification of genetic profiles associated with prostatic neoplasias that are more likely to result in aggressive disease may lead to improved management of prostate cancer patients. ..

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..Potential moderators/mediators include education, family structure, and quality of the family environment. ..

..The knowledge gained from this study would have direct bearing on efforts to improve care in PACE programs, as well as implications for other programs serving frail, non-institutionalized elderly. ..