scholarly journals A Powerful Approach for Identification of Differentially Transcribed mRNA Isoforms

2014 ◽  
Author(s):  
Yuande Tan
Keyword(s):  
Statistical Analysis ◽  
Statistical Methods ◽  
Count Data ◽  
Differentially Expressed Gene ◽  
Small Sample ◽  
T Test ◽  
Test Method ◽  
Differentially Expressed ◽  
Next Generation ◽  
Mrna Isoforms

Next generation sequencing is being increasingly used for transcriptome-wide analysis of differential gene expression. The primary goal in profiling expression is to identify genes or RNA isoforms differentially expressed between specific conditions. Yet, the next generation sequence-based count data are essentially different from the microarray data that are continuous type, therefore, the statistical methods developed well over the last decades cannot be applicable. For this reason, a variety of new statistical methods based on count data of transcript reads has been correspondingly developed. But currently the transcriptomic count data coming only from a few replicate libraries have high technical noise and small sample size bias, performances of these new methods are not desirable. We here developed a new statistical method specifically applicable to small sample count data called mBeta t-test for identifying differentially expressed gene or isoforms on the basis of the Beta t-test. The results obtained from simulated and real data showed that the mBeta t-test method significantly outperformed the existing statistical methods in all given scenarios. Findings of our method were validated by qRT-PCR experiments. The mBeta t-test method significantly reduced true false discoveries in differentially expressed genes or isoforms so that it had high work efficiencies in all given scenarios. In addition, the mBeta t-test method showed high stability in performance of statistical analysis and in estimation of FDR. These strongly suggests that our mBeta t-test method would offer us a creditable and reliable result of statistical analysis in practice.

scholarly journals Discriminative feature of cells characterizes cell populations of interest by a small subset of genes

2021 ◽  
Author(s):  
Takeru Fujii ◽  
Kazumitsu Maehara ◽  
Masatoshi Fujita ◽  
Yasuyuki Ohkawa
Keyword(s):  
Gene Expression ◽  
Statistical Methods ◽  
Cell Population ◽  
Differentially Expressed Gene ◽  
Adaptive Lasso ◽  
Differentially Expressed ◽  
Small Subset ◽  
Specific Gene ◽  
Large Sample Size ◽  
Discriminative Feature

ABSTRACTStatistical methods for detecting differences in individual gene expression are indispensable for understanding cell types. However, conventional statistical methods have faced difficulties associated with the inflation of P-values because of both the large sample size and selection bias introduced by exploratory data analysis such as single-cell transcriptomics. Here, we propose the concept of discriminative feature of cells (DFC), an alternative to using differentially expressed gene-based approaches. We implemented DFC using logistic regression with an adaptive LASSO penalty to perform binary classification for the discrimination of a population of interest and variable selection to obtain a small subset of defining genes. We demonstrated that DFC prioritized gene pairs with non-independent expression using artificial data, and that DFC enabled to characterize the muscle satellite cell population. The results revealed that DFC well captured cell-type-specific markers, specific gene expression patterns, and subcategories of this cell population. DFC may complement differentially expressed gene-based methods for interpreting large data sets.

scholarly journals Comparison of statistical methods for analysis of small sample sizes for detecting the differences in efficacy between treatments for knee osteoarthritis

2020 ◽  
Author(s):  
Chia-Lung Shih ◽  
Te-Yu Hung
Keyword(s):  
Knee Osteoarthritis ◽  
Sample Size ◽  
Statistical Methods ◽  
Statistical Power ◽  
Permutation Test ◽  
Small Sample Size ◽  
Small Sample ◽  
T Test ◽  
Sample Sizes ◽  
Knee Oa

Abstract Background A small sample size (n < 30 for each treatment group) is usually enrolled to investigate the differences in efficacy between treatments for knee osteoarthritis (OA). The objective of this study was to use simulation for comparing the power of four statistical methods for analysis of small sample size for detecting the differences in efficacy between two treatments for knee OA. Methods A total of 10,000 replicates of 5 sample sizes (n=10, 15, 20, 25, and 30 for each group) were generated based on the previous reported measures of treatment efficacy. Four statistical methods were used to compare the differences in efficacy between treatments, including the two-sample t-test (t-test), the Mann-Whitney U-test (M-W test), the Kolmogorov-Smirnov test (K-S test), and the permutation test (perm-test). Results The bias of simulated parameter means showed a decreased trend with sample size but the CV% of simulated parameter means varied with sample sizes for all parameters. For the largest sample size (n=30), the CV% could achieve a small level (<20%) for almost all parameters but the bias could not. Among the non-parametric tests for analysis of small sample size, the perm-test had the highest statistical power, and its false positive rate was not affected by sample size. However, the power of the perm-test could not achieve a high value (80%) even using the largest sample size (n=30). Conclusion The perm-test is suggested for analysis of small sample size to compare the differences in efficacy between two treatments for knee OA.

scholarly journals PENGARUH EXERCISE THERAPY MENGGUNAKAN PROVOKING ANKLE STRATEGY DAN COORDINATION THERAPY TERHADAP TINGKAT KELINCAHAN PEMAIN FUTSAL DI KOTA MALANG PASCA CEDERA SPRAIN ANKLE

2018 ◽  
Vol 2 (1) ◽  
pp. 1-12
Author(s):  
Achmad - Mahfud ◽  
Slamet Raharjo ◽  
Surendra Surendra
Keyword(s):  
Statistical Analysis ◽  
Exercise Therapy ◽  
Sampling Technique ◽  
T Test ◽  
Ankle Injury ◽  
Test Method ◽  
Paired Sample ◽  
Ankle Strategy ◽  
Therapy Effect ◽  
Sprain Ankle

 This is due to the rehabilitation is not followed by the exercise therapy. effect of exercise therapy using provoking ankle strategy and coordination therapy on the futsal player agility after sprained ankle injury. Study was conducted in Malang City. This research used pre-experimental One group pretest posttest design with the Total sampling technique. Research samples were 4 patients in Physioset Malang City who suffered from sprained ankle. The data were collected using the Illionis Agility Test, and then analyzed by using Paired sample t-test method. The result of statistical analysis (t-Test) on the agility data demonstrated the significance value of 0.016 (< α 0.05). Therefore, it can be stated that the research hypothesis was accepted. In other words, treatment therapy has a significant effect on the agility of futsal players in Physioset Malang City.

scholarly journals Methodology of statistical study of the chemical composition of by-products of coal mining to assess their suitability as materials for reclamation

2016 ◽  
Vol 32 (4) ◽  
pp. 73-90
Author(s):  
Jacek Mucha ◽  
Beata Klojzy-Karczmarczyk ◽  
Janusz Mazurek
Keyword(s):  
Statistical Analysis ◽  
Statistical Methods ◽  
Sulfur Content ◽  
Coal Mine ◽  
Total Content ◽  
Small Sample ◽  
Total Sulfur ◽  
Allowable Limit ◽  
Probability Of Error ◽  
Limit Values

Abstract The results of the research presented in earlier works with the participation of the authors (Klojzy-Karczmarczyk et al. 2016a, b, c) indicate the possibility of the use of mining waste from Janina Coal Mine (Upper Silesian Coal Basin, Poland, TAURON Wydobycie S.A.) or products (aggregates) produced on the basis of gangue for technical reclamation. It is essential for this process to obtain a material with low total sulfur, and it has been shown that the best quality parameters are obtained for the material subjected to modification by the rejection of fine fractions. In this work, the lower limit of the material’s fraction was determined using statistical analysis, wherein with the predetermined but low probability of error, the content of contaminants (sulfur, as well as other elements) does not exceed the allowable limit (reference value). To solve this task, 3 different statistical methods were used: evaluation of guaranteed contents (the maximum for a given degree of probability) of the polluting components, the results of statistical hypotheses testing and analysis of correlation and regression. The applied statistical methods produce results very proximate to each other. In the presented case study for the Janina coal mine based on the results of a statistically small sample (<30 observations) rock material fraction> 20 mm may be considered as safe for the purposes of reclamation, and the material fraction >25 mm as very safe. It cannot be ruled out, however, that this limit may be reduced to a diameter of 16 mm. The content analysis of 11 elements (As, Cd, Co, Cr, Cu, Hg, Mo, Ni, Pb, V, Zn determined as total content in the secondary samples for the fraction 10-200 mm (the fraction >200 mm was not present) showed that they are lower than the allowable limits specified by relevant legal regulations. For this fraction, exceedance of the limit values of sulfur content is, however, highly probable. For this reason, the primary criterion for determining the suitability of the waste material for the purposes of reclamation should be the total sulfur content, and the determination of the lower limits of the material fraction that meets the environmental requirements should be conducted using statistical methods based on the results of experimental sampling of rock remaining after coal preparation. The use of advanced methods of statistical analysis may facilitate the design of technological processes, leading to obtain industrial quantities of high quality, appropriately graded reclamation material.

Prediction of Thalidomide Response in the Newly Diagnosed Untreated Multiple Myeloma Patients Based on a Panel of Protein Biomarkers

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 5018-5018
Author(s):  
Rajpal Rajpal ◽  
Paul Dowling ◽  
Justine Meiller ◽  
Kenneth C Anderson ◽  
Philip Murphy ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Statistical Analysis ◽  
Statistical Significance ◽  
Internal Standard ◽  
T Test ◽  
Differentially Expressed ◽  
Clinical Samples ◽  
Newly Diagnosed ◽  
Serum Samples ◽  
2D Dige

Abstract Background: Multiple Myeloma (MM) is an incurable plasma cell malignancy. Recently, there have been major therapeutic advances in the treatment of MM, including the use of immunomodulatory drugs. Thalidomide alone or in combination represents an effective treatment strategy for newly diagnosed, relapsed and refractory MM patients. The identification of novel biomarkers could lead to more effective, individualized therapeutic strategies with improved patient outcomes. Patients, Method & Material: Serum samples of sixteen newly diagnosed multiple myeloma patients, who had had initial treatment with thalidomide based regimens were analyzed. Based on D100 re-staging, 8 responders and 8 non responders to thalidomide were identified. Samples were analysed using 2D-DIGE, a technique based on pre-electrophoretic labelling of samples with one of three spectrally resolvable fluorescent CyDyes (Cy2, Cy3, and Cy5) allowing multiplexing of samples into the same gel. Initially serum samples were immunodepleted, which specifically removes 14 high-abundant proteins representing approximately 94% of total protein mass. This allowed for easier analysis of low abundance proteins, which are more likely to be a source of potential biomarkers. All 2D-DIGE images were scanned and collected on a Typhoon Fluorescent Imager. Pooled samples were used as an internal standard to quantify expression changes with statistical significance. Statistics and quantitation of protein expression were carried out initially using DeCyder Biological Variation Analysis (BVA) software before performing subsequent Extended Data Analysis (EDA). Results: 18 proteins have been identified to be differentially expressed in non-responders compared to responders: 13 were up-regulated and 5 were down-regulated (t-test ≤ 0.02). All 18 proteins were &gt;1.25-fold differentially expressed, with changes up to 6.62-fold. For example, Fig.1 shows statistical analysis of protein 1 using DeCyder BVA software. This protein was increased 2.24-fold in the immuno-depleted serum from non-responders compared to responders, (t-test 0.0046). Once the 18 panel proteins were established, further statistical analysis was performed using DeCyder EDA software. Principal Components Analysis (PCA) was used to separate the responders from the non-responders based on the panel of 18 statistically significant differentially expressed proteins (Fig.2). Each dot on this plot represents a clinical sample; clinical samples from the same experimental groups are located in the same distinct areas, i.e. contained in one half of the plot, confirming consistency of results. Conclusion: Accurate prediction of an individual patient’s drug response is an important prerequisite of personalized medicine. Using a panel of proteomic biomarkers, we have demonstrated the feasibility of predicting sensitivity and response to thalidomide in previously untreated myeloma. We are in the process of identification of theses proteins and plan to confirm their predictive value in a larger group of patients. Figure Figure Figure Figure

scholarly journals A Survey of Accelerated Vibratory Fatigue Test Method of Aero-Engine Compressor Blading

1985 ◽  
Author(s):  
Tie-Ying Wu ◽  
Qi-Xin Lu
Keyword(s):  
Fatigue Test ◽  
Statistical Methods ◽  
Test Data ◽  
T Test ◽  
Test Method ◽  
Life Distribution ◽  
F Test ◽  
Aero Engine ◽  
Engine Compressor

In this paper, a new accelerated fatigue test (AFT) method based on Miner’s Law is advanced, which is used for vibratory fatigue test of aero-engine compressor blading. By using this method, a sample life distribution can be obtained and it saves time about 50–60%. This approach is validated by experiments and the test data are compared by two statistical methods — namely, F-test and t-test.

scholarly journals Peningkatan Atensi pada Anak ADHD dengan Teknik Self Instruction

2018 ◽  
Vol 2 (1) ◽  
pp. 27
Author(s):  
Fransisca Anindya Mariesta Prabawat ◽  
Niken Nurmei Ditasari
Keyword(s):  
Statistical Analysis ◽  
T Test ◽  
Test Method ◽  
Statistical Result ◽  
Adhd Children ◽  
Self Instruction ◽  
The Impact

<p>The aim of this study is to analyze the impact of self instruction method on attention improvement. Hypothesis of this study is self instruction method can increase attention of ADHD children.the subjects in this study are children which have been diagnosed with ADHD withage of  12 years old. Three behavior are observed, they are keep attention to the teacher, follow the teacher expression, and do the task until done according to teacher asking without leaving the chair.  ABA design was used as study’s design. Statistical analysis in the study was done using t-test method. Based on statistical result it was found that to t<sub>0 </sub>(5,143) &gt;t<sub>tab</sub>(2, 145) which can be concluded that treatment with self instruction method was significantly increase the attention of ADHD children.</p>

scholarly journals The Influence of Motivation, Discipline, Work Satisfaction and Company Environment to Employees Performance of PT Profab Indonesia

2019 ◽  
Author(s):  
Decky Antony Kifta
Keyword(s):  
Statistical Analysis ◽  
Statistical Methods ◽  
Descriptive Analysis ◽  
Work Satisfaction ◽  
T Test ◽  
Multiple Linear Regressions ◽  
Independent Variables ◽  
Analytical Test ◽  
Coefficient Corrélation ◽  
Linear Regressions

The purpose of this study is to understand the influence between motivation, discipline, work satisfaction and company environment with employees performance in PT Profab Indonesia. As understood that employees are company’s asset therefore improving employee’s performance will lead to improvement of company’s productivity. There are four elements or variables which are believed to influence employee’s performance. These variables are motivation, discipline, work satisfaction and company environment. To obtain the required data, the observer used some methods such as interviews, observations and distributing the questionnaires. The questionnaires were made based on the four independent variables and one dependent variable. There were 200 employees selected as respondents to fill the questionnaires, and the data obtained were analyzed using SPSS program. Tests were made using statistical methods i.e. descriptive analysis, prerequisite analytical test, t-test, F-test, multiple linear regressions and coefficients determination. The results obtained from the statistical analysis gives the conclusion and proves that there was significant correlation between the motivation, discipline, work satisfaction and company environment with employee’s performance either partially or simultaneously. This was shown in coefficient correlation value of 0.919 which is equal to ‘very strong’ and the value of adjusted R square of 0.841 or 84.1%, which means that the influence of motivation, discipline, work satisfaction and company environment toward employees’ performance is very strong, with the percentage of 84.1%.

scholarly journals Impact of Using Technology in Auditing on Reducing the Fees of Auditors Offices and Companies in Jordan

2019 ◽  
Vol 14 (8) ◽  
pp. 1
Author(s):  
Ali Mustafa Magablih
Keyword(s):  
Statistical Analysis ◽  
Standard Deviation ◽  
Statistical Methods ◽  
Analytical Approach ◽  
Audit Fees ◽  
T Test ◽  
Data Output ◽  
High Degree ◽  
The Impact ◽  
Methods Of Application

The current study aimed to identify the impact of using technology in auditing on reducing the fees of the auditors offices and companies operating in Jordan. To achieve this objective, the study adopted the descriptive analytical approach due to its suitability to the nature of the study. A questionnaire was adopted as the study tool where 280 questionnaires were distributed to the study sample, 216 were retrieved and 184 were analyzed after excluding 32 questionnaires since they were invalid for the statistical analysis. The researcher used some appropriate statistical methods such as T test, mean and standard deviation. The study had many results, most important of which are that using technology has an impact on reducing the audit fees for the auditor offices and companies due to its accuracy in data output and tabulation, and that the auditor practices the E-auditing efficiently since he realizes its various benefits for the audit offices and companies operating in Jordan, and they applied it to a high degree. The study recommended the need for the audit offices and companies to continue operating in Jordan through e-auditing and they should work on developing their methods of application.

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