724 research outputs found
Reproducible computing with rctrack: Software package addresses fundamental scientific challenges of Big Data era.
No full textPublished descriptions of data sets and analysis procedures are helpful ways to ensure scientific results are reproducible. Unfortunately the collection and provision of this information is often provided by researchers in retrospect and can be fraught with uncertainty. The only solution to this problem is to computationally collect and archive data files, code files, result files, and other details while the data analysis is being performed. Stan Pounds highlights the release of rctrack, a software package that automatically enables this file collection for analyses performed with the open-source R programming language, thereby minimizing the burden of collecting and archiving details
BIOINFORMATICS Sample Size Determination for the False Discovery Rate
No full textMotivation There is not a widely applicable method to determine the sample size for experiments basing statistical significance on the false discovery rate (FDR). Results We propose and develop the anticipated false discovery ratio (aFDR) as a conceptual tool for determining sample size. We derive mathematical expressions for the aFDR and anticipated average statistical power. These expressions are used to develop a general algorithm to determine sample size. We provide specific details on how to implement the algorithm for a k-group (k ≥ 2) comparisons. The algorithm performs well for k-group comparisons in a series of traditional simulations and in a real data simulation conducted by resampling from a large, publicly available data set. Availability Documented S-plus and R code libraries are freely available from www.stjuderesearch.org/depts/biostats. Contact: Stan Pounds
A Look at Philosophical Analysis
No full textThe author of this article, Dr. Ralph L. Pounds, is the author of many books and a Professor of Education at the University of Cincinnati. This article was first given as the presidential address of the Ohio Valley Philosophy of Education Society
Donny MacVane, 79, of Long Island, and his sons, Stan, Tom, and Lee, all fish fr
No full textDonny MacVane, 79, of Long Island, and his sons, Stan, Tom, and Lee, all fish from a pier MacVane built of pieces partly salvaged from the World War II Navy dock on the island. MacVane, who was born in his home, has lobstered all his life and remembers one August in the 1950s when he caught 20,000 pounds of lobster. He says fishermen now are more harvesters than fishermen. With details on his fishing life and the innovations he brought to his work
Reference Alignment of SNP Microarray Signals for Copy Number Analysis of Tumors
No full textA new procedure to align single-nucleotide polymorphism (SNP) microarray signals for copy number analysis is proposed. For each individual array, this reference alignment procedure (RAP) uses a set of selected markers as internal references to direct the signal alignment. RAP aligns the signals so that each array has a similar signal distribution among its reference markers. An accompanying reference selection algorithm (RSA) uses genotype calls and initial signal intensities to choose two-copy markers as the internal references for each array. After RSA and RAP are applied, each array has a similar distribution of signals of two-copy markers so that across-array signal comparisons are biologically meaningful. An upper bound for a statistical metric of signal misalignment is derived and provides a theoretical basis to choose RSA-RAP over other alignment procedures for copy number analysis of cancers. In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures
Patient-centred communication in Ask-the-expert healthcare websites
No full textThe study presented in this article explores to what extent and in what ways the communication between clinicians and patients on Ask-the-Expert healthcare websites is patient-centred. It further demonstrates the value of using a theory- and text-driven discourse analytical approach for the analysis of verbal communication in a (specific health) professional domain. The UK website Netdoctor is used as a case study. Thirty exchanges from this site, on the topic of depression, were analysed using a discourse-pragmatic framework, drawing on existing theories and definitions of patient-centred communication (PCC), a classification of empathic communication acts (Pounds 2011) and existing research on advice-giving in online communication. The analysis shows that, overall, experts make wide use of PCC, particularly empathic expression, in their online responses. The author concludes that there is a high potential for the expression of PCC on Ask-the-Expert health sites and that this may be more or less exploited, depending on the restrictions imposed on the contributors by the site managers and users’ expectation
Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data
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An R package that automatically collects and archives details for reproducible computing
No full textAn Economic Analysis of Electron Accelerators and Cobalt-60 for Irradiating Food
No full textAverage costs per pound of irradiating food are similar for the electron accelerator and cobalt-60 irradiators analyzed in this study, but initial investment costs can vary by $1 million. Irradiation costs range from 0.5 to 7 cents per pound and decrease as annual volumes treated increase. Cobalt-60 is less expensive than electron beams for annual volumes below 50 million pounds. For radiation source requirements above the equivalent of 1 million curies of cobalt-60, electron beams are more economical.food irradiation, electron accelerators, cobalt-60, cost comparison, economies of size, Food Consumption/Nutrition/Food Safety,
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