Biplots in biomedical research

Gabriel, K. Ruben; Odoroff, Charles L.

doi:10.1002/sim.4780090502

Cited by 159 publications

(87 citation statements)

References 11 publications

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“…A Biplot analysis (Gabriel, 1971;Gabriel and Odoroff, 1990;Gower and Hand, 1996) allows for the simultaneous representation of individuals (rows) and variables (columns) of a numerical data matrix in a low dimensional space. Gabriel (1971) proposed two different analyses: JKBiplot and GH-Biplot.…”

Section: Discussionmentioning

confidence: 99%

Benefit of ancillary data acquired at the cooperative level to study soil type and climatic zone influence on berry composition: a case study in Rioja appellation

et al. 2018

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Aim:The main objective of this study was to evaluate the influence of soil type and climate on must qualitative parameters in a winegrower's cooperative at Rioja appellation. Methods and results:The study was conducted from 2009 to 2011 with data collected routinely before harvest by the technician of a cooperative with a total surface area of 525 ha. Soils were classified using an existing soil map (1:50.000 scale) according to their water-holding capacity (WHC), and two climatic zones were differentiated based on the Huglin index. Effects of soil and climate on berry composition were evaluated using HJ-Biplot statistical analysis. High WHC soils produced musts with high total acidity, mainly due to malic acid. Must K concentrations were lower in soils with lower K and clay content. Soils with lower WHC were the only ones able to produce musts with high anthocyanin concentration and higher colour intensity. The climatic zones established only resulted in small differences in grape composition. Conclusion:It is possible to differentiate berry composition parameters according to soil type considering soil WHC, but less clear differences were observed among climatic zones considering a 50 km 2 area and a difference of approximately 200 m in elevation between the two zones.Significance and impact of the study: Many wineries have access to soil, climate and grape composition data. Therefore, these data could be used to make a grape composition classification at harvest that could be assessed every year using simple statistical tools.

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Section: Discussionmentioning

confidence: 99%

Benefit of ancillary data acquired at the cooperative level to study soil type and climatic zone influence on berry composition: a case study in Rioja appellation

et al. 2018

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“…The level of gene expression could be displayed in a database using parallel coordinate plots [175,176] produced by the lattice package in R (version 2.9.0, The R Foundation for Statistical Computing [http://cran.r-project.org], and S-plus software (Insightful Corporation, Seattle, WA). Other packages such as GESS (Gene Expression Statistical System) published by NCSS [http://www.ncss.com] could also be employed, as needed Bioinformatics analysis using the basic TargetScan algorithm [103] for up-regulated and down regulated mRNAs genes has been employed.…”

Section: Statistical Methods and Bioinformatics Analysesmentioning

confidence: 99%

MicroRNAs as molecular markers for colon cancer Diagnostic screening in stool & blood

Ahmed¹,

Ahmed²

2017

Med Res Innov

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Screening for colon cancer (CC) allows for diagnosis of the early stage for malignancy and potentially reduces disease mortality as the cancer could be cured at disease earliest stages. Early detection could be desirable if accurate, practical and cost effective diagnostic measures for this cancer are available. Mortality and morbidity from colon cancer represent a major health problem involving a malignant disease that is theoretically preventable through screening. Current screening methods (e.g., the immunological fecal occult blood test, FOBTi, obtained from patients' medical records) either lacks sensitivity and requires dietary restriction, which impedes compliance and use; are costly (e.g., colonoscopy), which decreases compliance; or could lead to mortality. In comparison to the FOBT test, a noninvasive sensitive screen for which there is no requirement for dietary restriction would be a more convenient test. Colorectal cancer (CRC) is the only cancer for which screening by colonoscopy is recommended. Although colonoscopy is a reliable screening tool, its invasive nature, accompanying abdominal pain, potential complications and high cost have hampered the application of this screening method worldwide.A novel screening approach using the stable miRNA molecules, which are relatively nondegradable when extracted from noninvasive stool and semi-invasive blood samples by currently available commercial kits and manipulated thereafter, would be preferable to a transcriptomic messenger (m)RNA-, a mutation DNA-, an epigenetic-or a proteomic-based test. The approach utilizes reverse transcriptase (RT), followed by a modified quantitative real-time polymerase chain reaction (qPCR). Although exosomal RNA would not be measured, using a restricted extraction of total RNA from stool or blood, then a parallel test could also be carried out on RNA obtained from stool or plasma samples, and appropriate corrections for exsosomal loss can be made to obtain accurate and quantitative results. Eventually, a chip would be developed to facilitate diagnosis, as has been carried out for the quantification of genetically modified organisms (GMOs) in foods. The gold standard to which the molecular miRNA test is compared is colonoscopy. If performance criteria are met, as detailed herein, then a miRNA test in human stool or blood samples based on high throughput automated technologies and quantitative expression measurements --commonly used in the diagnostic clinical laboratory--would eventually be advanced to the clinical setting, which will make a vivid impact on the prevention of colon cancer.Correspondence to: Farid E. Ahmed, GEM

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“…22 This method provides a graphical summary of correlations through the overlaid display of two plots: one for correlations among subjects and another for correlations among variables. 23 We considered the mechanism behind missing values for each variable and then examined the proportion of values missing for each variable as well as patterns of missing values across variables. Multiple imputation with chained equations was used with 10 imputed data sets when a desired predictor was <25% missing in both trial and registry.…”

Section: Analytic Methodsmentioning

confidence: 99%

Assessing the applicability of trial evidence to a target sample in the presence of heterogeneity of treatment effect

Weiss

Segal

Varadhan

2012

Pharmacoepidemiology and Drug

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Purpose To propose methods for the quantitative assessment of the applicability of evidence from a trial to a target sample using individual data. Methods Demonstration was with a trial of drug therapy to prevent mortality and an accompanying registry of people with heart failure. Principal components analysis with biplots did not identify measurement discrepancies. Multiple imputation with chained equations addressed missing predictor values. A proportional hazards model with interaction term, including graphical interpretation and a multivariate interaction test, identified heterogeneity of treatment effect. An interval of homogeneity of treatment effect was the interval of the baseline risk of outcome in which no two treatment effects were statistically significantly different. Absolute risk reduction for individuals was estimated for both benefit and harm outcomes and presented in a bivariate treatment effects scatterplot. Results Overall, the trial evidence applied to most of the registry according to overlapping distributions of estimated benefit and harm. However, 52% of trial and 33% of registry participants were estimated to have net benefit, and 14% of trial and 36% of registry participants were estimated to have strong net harmful treatment effect, that is, the individual estimate of harm was more than twice the estimate of benefit. Conclusions The proposed methods provide quantitative assessment of the applicability of trial evidence to a target sample. They combine the strengths of different study designs, namely, unbiased effects estimation from trials and representation in observational studies, while addressing the practical challenges of combining information, namely, measurement discrepancies and missing data.

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Biplots in biomedical research

Cited by 159 publications

References 11 publications

Benefit of ancillary data acquired at the cooperative level to study soil type and climatic zone influence on berry composition: a case study in Rioja appellation

Benefit of ancillary data acquired at the cooperative level to study soil type and climatic zone influence on berry composition: a case study in Rioja appellation

MicroRNAs as molecular markers for colon cancer Diagnostic screening in stool & blood

Assessing the applicability of trial evidence to a target sample in the presence of heterogeneity of treatment effect

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