Adjusting Batch Effects in Microarray Experiments with Small Sample Size Using Empirical Bayes Methods

2009 ◽  
pp. 113-129 ◽  
Author(s):  
W Evan Johnson ◽  
Cheng Li
Keyword(s):  
Sample Size ◽  
Empirical Bayes ◽  
Small Sample Size ◽  
Small Sample ◽  
Batch Effects ◽  
Microarray Experiments ◽  
Bayes Methods ◽  
Empirical Bayes Methods

scholarly journals Perbandingan Metode Bootstrap, Jacknife Jiang Dan Area Specific Jacknife Pada Pendugaan Mean Square Error Model Beta-Bernoulli

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Yesi Santika ◽  
◽  
Widiarti Widiarti ◽  
Fitriani Fitriani ◽  
Mustofa Usman ◽  
...  
Keyword(s):  
Sample Size ◽  
Mean Square Error ◽  
Small Area ◽  
Empirical Bayes ◽  
Mean Squared Error ◽  
Small Sample Size ◽  
Statistical Technique ◽  
Small Sample ◽  
Mean Square ◽  
The Mean

Small area estimation is defined as a statistical technique for estimating the parameters of a subpopulation with a small sample size. One method of estimating small area parameters is the Empirical Bayes (EB) method. The accuracy of the Empirical Bayes (EB) estimator can be measured by evaluating the Mean Squared Error (MSE). In this study, 3 methods to determine MSE in the EB estimator of the Beta-Bernoulli model will be compared, namely the Bootstrap, Jackknife Jiang and Area-specific Jackknife methods. The study is carried out theoretically and empirically through simulation with R-studio software version 1.2.5033. The simulation results in a number of areas and pairs of prior distribution parameter values, namely Beta, show the effect of sample size and parameter value pairs on the Mean Square Error (MSE) value. The larger the number of areas and the smaller the initial 𝛽, the smaller the MSE value. The area-specific Jackknife method produces the smallest MSE in the number of areas 100 and the Beta parameter value 0.1.

Application of Ultrasound Elastography for Assessing Intestinal Fibrosis in Inflammatory Bowel Disease: Fiction or Reality?

2020 ◽  
Vol 21 ◽  
Author(s):  
Roberto Gabbiadini ◽  
Eirini Zacharopoulou ◽  
Federica Furfaro ◽  
Vincenzo Craviotto ◽  
Alessandra Zilli ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Sample Size ◽  
Bowel Disease ◽  
Small Sample Size ◽  
Shear Wave Elastography ◽  
Small Sample ◽  
Ultrasound Elastography ◽  
Invasive Technique ◽  
Intestinal Fibrosis ◽  
Inflammatory Bowel

Background: Intestinal fibrosis and subsequent strictures represent an important burden in inflammatory bowel disease (IBD). The detection and evaluation of the degree of fibrosis in stricturing Crohn’s disease (CD) is important to address the best therapeutic strategy (medical anti-inflammatory therapy, endoscopic dilation, surgery). Ultrasound elastography (USE) is a non-invasive technique that has been proposed in the field of IBD for evaluating intestinal stiffness as a biomarker of intestinal fibrosis. Objective: The aim of this review is to discuss the ability and current role of ultrasound elastography in the assessment of intestinal fibrosis. Results and Conclusion: Data on USE in IBD are provided by pilot and proof-of-concept studies with small sample size. The first type of USE investigated was strain elastography, while shear wave elastography has been introduced lately. Despite the heterogeneity of the methods of the studies, USE has been proven to be able to assess intestinal fibrosis in patients with stricturing CD. However, before introducing this technique in current practice, further studies with larger sample size and homogeneous parameters, testing reproducibility, and identification of validated cut-off values are needed.

scholarly journals Confirming known planetary trends using a photometrically selected Kepler sample

2020 ◽  
Author(s):  
Jonah T Hansen ◽  
Luca Casagrande ◽  
Michael J Ireland ◽  
Jane Lin
Keyword(s):  
Sample Size ◽  
Robust Statistics ◽  
Narrow Band ◽  
Small Sample Size ◽  
Small Sample ◽  
Fitting Algorithm ◽  
Statistical Studies ◽  
The Rich ◽  
Host Stars ◽  
High Metallicity

Abstract Statistical studies of exoplanets and the properties of their host stars have been critical to informing models of planet formation. Numerous trends have arisen in particular from the rich Kepler dataset, including that exoplanets are more likely to be found around stars with a high metallicity and the presence of a “gap” in the distribution of planetary radii at 1.9 R⊕. Here we present a new analysis on the Kepler field, using the APOGEE spectroscopic survey to build a metallicity calibration based on Gaia, 2MASS and Strömgren photometry. This calibration, along with masses and radii derived from a Bayesian isochrone fitting algorithm, is used to test a number of these trends with unbiased, photometrically derived parameters, albeit with a smaller sample size in comparison to recent studies. We recover that planets are more frequently found around higher metallicity stars; over the entire sample, planetary frequencies are 0.88 ± 0.12 percent for [Fe/H] < 0 and 1.37 ± 0.16 percent for [Fe/H] ≥ 0 but at two sigma we find that the size of exoplanets influences the strength of this trend. We also recover the planet radius gap, along with a slight positive correlation with stellar mass. We conclude that this method shows promise to derive robust statistics of exoplanets. We also remark that spectrophotometry from Gaia DR3 will have an effective resolution similar to narrow band filters and allow to overcome the small sample size inherent in this study.

scholarly journals The use of diversity indices for local assessment of marine sediment quality

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shinya Hosokawa ◽  
Kyosuke Momota ◽  
Anthony A. Chariton ◽  
Ryoji Naito ◽  
Yoshiyuki Nakamura
Keyword(s):  
Community Structure ◽  
Sample Size ◽  
Small Sample Size ◽  
Benthic Communities ◽  
Sediment Quality ◽  
Diversity Indices ◽  
Small Sample ◽  
Species Density ◽  
Local Case ◽  
Two Indices

AbstractDiversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.

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