Marginal Correlation from Logit- and Probit-Beta-Normal Models for Hierarchical Binary Data

In hierarchical data settings, be it of a longitudinal, spatial, multi-level, clustered, or otherwise repeated nature, often the association between repeated measurements attracts at least part of the scientific interest. Quantifying the association frequently takes the form of a correlation function, including but not limited to intraclass correlation. Vangeneugden et al. (2010 Vangeneugden, T., Molenberghs, G., Laenen, A., Geys, H., Beunckens, C., Sotto, C. (2010). Marginal correlation in longitudinal binary data based on generalized linear mixed models. Communi. Stati. Theory &; Methods. 39:3542–3557. [Google Scholar]) derived approximate correlation functions for longitudinal sequences of general data type, Gaussian and non-Gaussian, based on generalized linear mixed-effects models. Here, we consider the extended model family proposed by Molenberghs et al. (2010 Molenberghs, G., Verbeke, G., Demétrio, C., Vieira, A. (2010). A family of generalized linear models for repeated measures with normal and conjugate random effects. Stat. Sci. 25:325–347.[Crossref], [Web of Science ®] , [Google Scholar]). This family flexibly accommodates data hierarchies, intra-sequence correlation, and overdispersion. The family allows for closed-form means, variance functions, and correlation function, for a variety of outcome types and link functions. Unfortunately, for binary data with logit link, closed forms cannot be obtained. This is in contrast with the probit link, for which such closed forms can be derived. It is therefore that we concentrate on the probit case. It is of interest, not only in its own right, but also as an instrument to approximate the logit case, thanks to the well-known probit-logit ‘conversion.’ Next to the general situation, some important special cases such as exchangeable clustered outcomes receive attention because they produce insightful expressions. The closed-form expressions are contrasted with the generic approximate expressions of Vangeneugden et al. (2010 Vangeneugden, T., Molenberghs, G., Laenen, A., Geys, H., Beunckens, C., Sotto, C. (2010). Marginal correlation in longitudinal binary data based on generalized linear mixed models. Communi. Stati. Theory &; Methods. 39:3542–3557. [Google Scholar]) and with approximations derived for the so-called logistic-beta-normal combined model. A simulation study explores performance of the method proposed. Data from a schizophrenia trial are analyzed and correlation functions derived.     

Optimality of ratio type estimation methods for population mean in the presence of missing data

This article proposes various Searls-type ratio imputation methods (STRIM) on the lines of Ahmed et al. (2006 Ahmed, M. S., O. Al-Titi, Z. Al-Rawi, and W. Abu-Dayyeh. 2006. Estimation of a population mean using different imputation methods. Stat. Trans. 7 (6):1247–1264. [Google Scholar]). It is a well-known fact that the optimal ratio type estimator attains the MSE of regression estimator (or optimal difference estimator) but while using Searls-type transformation (STT) (Searls (1964 Searls, D. T. 1964. The utilization of a known coefficient of variation in the estimation procedure. J. Am. Stat. Assoc. 59:1225–1226.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar])) this may not always happen. These STRIM are shown to perform better than the imputation procedures of Ahmed et al. (2006 Ahmed, M. S., O. Al-Titi, Z. Al-Rawi, and W. Abu-Dayyeh. 2006. Estimation of a population mean using different imputation methods. Stat. Trans. 7 (6):1247–1264. [Google Scholar]). The STRIM may even outperform the Searls type difference imputation methods (STDIM) proposed by us in our earlier work, Bhushan and Pandey (2016 Bhushan, S., and A. P. Pandey. 2016. Optimal imputation of the missing data for estimation of population mean. Journal of Statistics and Management System 19 (6):755–69.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]). This study is concluded with the numerical study along with the theoretical comparison.     

A Bayesian control chart for a common coefficient of variation

By using the medical data analyzed by Kang et al. (2007 Kang, C.W., Lee, M.S., Seong, Y.J., Hawkins, D.M. (2007). A control chart for the coefficient of variation. J. Qual. Technol. 39(2):151–158.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), a Bayesian procedure is applied to obtain control limits for the coefficient of variation. Reference and probability matching priors are derived for a common coefficient of variation across the range of sample values. By simulating the posterior predictive density function of a future coefficient of variation, it is shown that the control limits are effectively identical to those obtained by Kang et al. (2007 Kang, C.W., Lee, M.S., Seong, Y.J., Hawkins, D.M. (2007). A control chart for the coefficient of variation. J. Qual. Technol. 39(2):151–158.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]) for the specific dataset they used. This article illustrates the flexibility and unique features of the Bayesian simulation method for obtaining posterior distributions, predictive intervals, and run-lengths in the case of the coefficient of variation. A simulation study shows that the 95% Bayesian confidence intervals for the coefficient of variation have the correct frequentist coverage.     

Adaptive tangent distance classifier on recognition of handwritten digits

Simard et al. [16 Simard, P. Y., LeCun, Y., Denker, J. S. and Victorri, B. 2000. Transformation invariance in pattern recognition: Tangent distance and tangent propagation. J. Imaging Syst. Technol., 11: 181–197.  [Google Scholar] 17 Sona, D., Sperduti, A. and Starita, A. 1997. A constructive learning algorithm for discriminant tangent models. Advances in Neural Information Processing Systems. 1997, Cambridge, MA. Edited by: Mozer, M. C., Jordan, M. I. and Petsche, T. Vol. 9, pp.786–792. MIT Press.  [Google Scholar]] proposed a transformation distance called “tangent distance” (TD) which can make pattern recognition be efficient. The key idea is to construct a distance measure which is invariant with respect to some chosen transformations. In this research, we provide a method using adaptive TD based on an idea inspired by “discriminant adaptive nearest neighbor” [7 Hastie, T., Tibshirani, R. and Friedman, J. 2009. The Elements of Statistical Learning, Data Mining, Inference, and Prediction, 2, New York, Berlin, Heidelberg: Springer. Available at http://www-stat.stanford.edu/ElemStatLearn [Google Scholar]]. This method is relatively easy compared with many other complicated ones. A real handwritten recognition data set is used to illustrate our new method. Our results demonstrate that the proposed method gives lower classification error rates than those by standard implementation of neural networks and support vector machines and is as good as several other complicated approaches.     

Bayesian Estimation for Linear Functions of Poisson Rates

The probability matching prior for linear functions of Poisson parameters is derived. A comparison is made between the confidence intervals obtained by Stamey and Hamilton (2006 Stamey, J., Hamilton, C. (2006). A note on confidence intervals for a linear function of Poisson rates. Commun. Statist. Simul. &; Computat. 35(4):849–856.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), and the intervals derived by us when using the Jeffreys’ and probability matching priors. The intervals obtained from the Jeffreys’ prior are in some cases fiducial intervals (Krishnamoorthy and Lee, 2010 Krishnamoorthy, K., Lee, M. (2010). Inference for functions of parameters in discrete distributions based on fiducial approach: Binomial and Poisson cases. J. Statist. Plann. Infere. 140(5):1182–1192.[Crossref], [Web of Science ®] , [Google Scholar]). A weighted Monte Carlo method is used for the probability matching prior. The power and size of the test, using Bayesian methods, is compared to tests used by Krishnamoorthy and Thomson (2004 Krishnamoorthy, K., Thomson, J. (2004). A more powerful test for comparing two Poisson means. J. Statist. Plann. Infere. 119(1):23–35.[Crossref], [Web of Science ®] , [Google Scholar]). The Jeffreys’, probability matching and two other priors are used.     

Complete convergence for coordinatewise asymptotically negatively associated random vectors in Hilbert spaces

In this article, we study the complete convergence for sequences of coordinatewise asymptotically negatively associated random vectors in Hilbert spaces. We also investigate that some related results for coordinatewise negatively associated random vectors in Huan, Quang, and Thuan (2014 Huan, N. V., N. V. Quang, and N. T. Thuan. 2014. Baum–Katz type theorems for coordinatewise negatively associated random vectors in Hilbert spaces. Acta Mathematica Hungarica 144(1):132–419.[Crossref], [Web of Science ®] , [Google Scholar]) still hold under this concept.     

Performance of some ridge regression estimators for the multinomial logit model

This article considers several estimators for estimating the ridge parameter k for multinomial logit model based on the work of Khalaf and Shukur (2005 Khalaf, G., and G. Shukur. 2005. Choosing ridge parameters for regression problems. Commun. Statist. Theor. Meth., 34:1177–1182.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), Alkhamisi et al. (2006 Alkhamisi, M., G. Khalaf, and G. Shukur. 2006. Some modifications for choosing ridge parameters. Commun. Statist. Theor. Meth. 35:2005–2020.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), and Muniz et al. (2012 Muniz, G., B. M. G. Kibria, K. Månsson, and G. Shukur. 2012. On developing ridge regression parameters: A graphical investigation. in SORT. 36: 115–138.[Web of Science ®] , [Google Scholar]). The mean square error (MSE) is considered as the performance criterion. A simulation study has been conducted to compare the performance of the estimators. Based on the simulation study we found that increasing the correlation between the independent variables and the number of regressors has negative effect on the MSE. However, when the sample size increases the MSE decreases even when the correlation between the independent variables is large. Based on the minimum MSE criterion some useful estimators for estimating the ridge parameter k are recommended for the practitioners.     

A new estimator of finite population mean based on the dual use of the auxiliary information

When a sufficient correlation between the study variable and the auxiliary variable exists, the ranks of the auxiliary variable are also correlated with the study variable, and thus, these ranks can be used as an effective tool in increasing the precision of an estimator. In this paper, we propose a new improved estimator of the finite population mean that incorporates the supplementary information in forms of: (i) the auxiliary variable and (ii) ranks of the auxiliary variable. Mathematical expressions for the bias and the mean-squared error of the proposed estimator are derived under the first order of approximation. The theoretical and empirical studies reveal that the proposed estimator always performs better than the usual mean, ratio, product, exponential-ratio and -product, classical regression estimators, and Rao (1991 Rao, T.J. (1991). On certail methods of improving ration and regression estimators. Commun. Stat. Theory Methods 20(10):3325–3340.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), Singh et al. (2009 Singh, R., Chauhan, P., Sawan, N., Smarandache, F. (2009). Improvement in estimating the population mean using exponential estimator in simple random sampling. Int. J. Stat. Econ. 3(A09):13–18. [Google Scholar]), Shabbir and Gupta (2010 Shabbir, J., Gupta, S. (2010). On estimating finite population mean in simple and stratified random sampling. Commun. Stat. Theory Methods 40(2):199–212.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]), Grover and Kaur (2011 Grover, L.K., Kaur, P. (2011). An improved estimator of the finite population mean in simple random sampling. Model Assisted Stat. Appl. 6(1):47–55. [Google Scholar], 2014) estimators.     

On dynamic weighted survival entropy of order α

Recently, Abbasnejad et al. (2010 Abbasnejad, M., Arghami, N.R., Morgenthaler, S., Mohtashami Borzadaran, G.R. (2010). On the dynamic survival entropy. Stat. Probab. Lett. 80:1962–1971.[Crossref], [Web of Science ®] , [Google Scholar]) proposed a measure of uncertainty based on survival function, called the survival entropy of order α. A dynamic form of the survival entropy of order α is also proposed by them. In this paper, we derive the weighted form of these measures. The properties of the new measures are also discussed.     

MODIFICATION OF KELLY AND RICE METHOD FOR SYNERGISM TESTS

ABSTRACT

In this paper, we present a modified Kelly and Rice method for testing synergism. This approach is consistent with Berenbaum's1-3 Berenbaum, M.C. 1977. Synergism, Additivism, and Antagonism in Immuno-Suppression: A Critical Review. Clinical and Experimental Immunology, 28: 1–18. Berenbaum, M.C. 1985. The Expected Effect of a Combination of Agents: The General Solution. Journal of Theoretical Biology, 114: 413–431. Berenbaum, M.C. 1989. What is Synergism? Pharmacological Reviews. 41: 93–141.   framework for additivity. The delta method[4] Bishop, Y.M., Fienberg, S.E. and Holland, P.W. 1975. Discrete Multivariate Analysis: Theory and Practice Massachusetts: MIT Press.  [Google Scholar] is applied to obtain the estimated variance for the predicted additivity proportion. A Monte Carlo simulation study for the evaluation of the method's performance, i.e., global overall tests for synergism, is also discussed. Kelly and Rice[5] Kelly, C. and Rice, J. 1990. Monotone Smoothing with Application to Dose-Response Curves and the Assessment of Synergism. Biometrics, 46: 1071–1085. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] do not provide a correct test statistic because the variance is underestimated. Hence, the performance of the Kelly–Rice[5] Kelly, C. and Rice, J. 1990. Monotone Smoothing with Application to Dose-Response Curves and the Assessment of Synergism. Biometrics, 46: 1071–1085. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] method is generally anti-conservative, based on the simulation findings. In addition, the overall test of synergism with χ²(r) from the modified Kelly and Rice method for larger sample sizes is better than that with χ²(1) from the modified Kelly and Rice method.     

Measures of predictor sensitivity for order-insensitive partitioning of multiple correlation

Lindeman et al. [12 Lindeman, R. H., Merenda, P. F. and Gold, R. Z. 1980. Introduction to Bivariate and Multivariate Analysis, Glenview, IL: Scott Foresman.  [Google Scholar]] provide a unique solution to the relative importance of correlated predictors in multiple regression by averaging squared semi-partial correlations obtained for each predictor across all p! orderings. In this paper, we propose a series of predictor sensitivity statistics that complement the variance decomposition procedure advanced by Lindeman et al. [12 Lindeman, R. H., Merenda, P. F. and Gold, R. Z. 1980. Introduction to Bivariate and Multivariate Analysis, Glenview, IL: Scott Foresman.  [Google Scholar]]. First, we detail the logic of averaging over orderings as a technique of variance partitioning. Second, we assess predictors by conditional dominance analysis, a qualitative procedure designed to overcome defects in the Lindeman et al. [12 Lindeman, R. H., Merenda, P. F. and Gold, R. Z. 1980. Introduction to Bivariate and Multivariate Analysis, Glenview, IL: Scott Foresman.  [Google Scholar]] variance decomposition solution. Third, we introduce a suite of indices to assess the sensitivity of a predictor to model specification, advancing a series of sensitivity-adjusted contribution statistics that allow for more definite quantification of predictor relevance. Fourth, we describe the analytic efficiency of our proposed technique against the Budescu conditional dominance solution to the uneven contribution of predictors across all p! orderings.     

Heavy traffic analysis of roving server networks

This article studies the heavy-traffic (HT) behavior of queueing networks with a single roving server. External customers arrive at the queues according to independent renewal processes and after completing service, a customer either leaves the system or is routed to another queue. This type of customer routing in queueing networks arises very naturally in many application areas (in production systems, computer- and communication networks, maintenance, etc.). In these networks, the single most important characteristic of the system performance is oftentimes the path time, i.e., the total time spent in the system by an arbitrary customer traversing a specific path. The current article presents the first HT asymptotic for the path-time distribution in queueing networks with a roving server under general renewal arrivals. In particular, we provide a strong conjecture for the system’s behavior under HT extending the conjecture of Coffman et al.^{[8 Coffman, Jr, E. G.; Puhalskii, A. A.; Reiman, M. I,. Polling systems with zero switchover times: A heavy-traffic averaging principle. Ann. App. Prob. 1995, 5(3), 681–719.[Crossref], [Web of Science ®] [Google Scholar],9 Coffman, Jr., E. G.; Puhalskii, A. A.; Reiman, M. I,. Polling systems in heavy-traffic: A Bessel process limit. Math. Oper. Res. 1998, 23, 257–304.[Crossref], [Web of Science ®] [Google Scholar]]} to the roving server setting of the current article. By combining this result with novel light-traffic asymptotics, we derive an approximation of the mean path time for arbitrary values of the load and renewal arrivals. This approximation is not only highly accurate for a wide range of parameter settings, but is also exact in various limiting cases.     

Characterization results based on dynamic Tsallis cumulative residual entropy

In this article, the concept of cumulative residual entropy (CRE) given by Rao et al. (2004 Rao, M., Chen, Y., Vemuri, B.C., Wang, F. (2004). Cumulative residual entropy: A new measure of information. IEEE Trans. Inf. Theory 50:1220–1228.[Crossref], [Web of Science ®] , [Google Scholar]) is extended to Tsallis entropy function and dynamic version, both residual and past of it. We study some properties and characterization results for these generalized measures. In addition, we provide some characterization results of the first-order statistic based on the Tsallis survival entropy.     

Edgeworth Expansion of the Moment-Based Test for Homogeneity in an NEF-QVF Mixture Model

In this article, we study the moment-based test procedure for a mixture distribution for the Natural exponential family with quadratic variance functions (NEF-QVF) family proposed by Ning et al. (2009b Ning, W., Zhang, S. G. and Yu, C. 2009b. A moment-based test for the homogeneity in mixture natural exponential family with quadratic variance functions. Statistical and Probability Letters, 79: 828–834. [Crossref] , [Google Scholar]) in the small sample size scenario. We derive the approximation for the null distribution of the test statistic by the Edgeworth expansion. The simulations are conducted for a binomial mixture distribution, which includes the situation corresponding to the detection of the linkage in the genetic analysis, with different sample sizes and family sizes at various significance levels. The simulation results show that our test performs reasonably well. We also apply the proposed method to the real clinical data to verify the significant difference between two drug treatments. The critical values associated with a binomial mixture distribution are also provided.     

Comparison of Frailty Models for Acute Leukemia Data under Gompertz Baseline Distribution

In this article, we consider two different shared frailty regression models under the assumption of Gompertz as baseline distribution. Mostly assumption of gamma distribution is considered for frailty distribution. To compare the results with gamma frailty model, we consider the inverse Gaussian shared frailty model also. We compare these two models to a real life bivariate survival data set of acute leukemia remission times (Freireich et al., 1963 Freireich, E.J., Gehan, E., Frei, E., Schroeder, L.R., Wolman, I.J., Anbari, R., Burgert, E.O., Mills, S.D., Pinkel, D., Selawry, O.S., Moon, J.H., Gendel, B.R., Spurr, C.L., Storrs, R., Haurani, F., Hoogstraten, B., Lee, S. (1963). The effect of 6-mercaptopurine on the duration of steroid-induced remissions in acute leukemia: a model for evaluation of other potentially useful therapy. Blood 21:699–716.[Web of Science ®] , [Google Scholar]). Analysis is performed using Markov Chain Monte Carlo methods. Model comparison is made using Bayesian model selection criterion and a well-fitted model is suggested for the acute leukemia data.     

On evaluating the performance of different forecasters

In this article, we have evaluated the performance of different forecasters and tested association between their performances for different pairs of variables. We have used three data sets of track records of professional U.S. economic forecasters participating in the Blue Chip consensus forecasting service (the data sets contain the root mean square errors (RMSE) of different forecasters for different years). To evaluate the performance of forecasters we have covered three well-known tests, namely the usual F test (cf. Fisher (1923 Fisher, R. A., Mackenzie, M. A. (1923). Studied in crop variation II. The manurial response of different potato. Journal of Agricultural Science 13:311–320. [Google Scholar])), Kruskal Wallis test (cf. Kruskal and Wallis (1952 Kruskall, W. H., Wallis, W. A. (1952). Use of ranks in one-criterion variance analysis. Journal of American Statistical Association 47:583–621. [Google Scholar])), and Extension of Median test (cf. Daniel (1990 Daniel, W. W. (1990). Applied Nonparametric Statistics. Duxbury Classic Series. (2nd Ed.), Boston. [Google Scholar])). To test the association between the forecaster's performances for different pairs of variables, we have considered Gini mean correlation coefficient r_g1 (cf. Yitzhaki, S., and Olkin, I. (1991 Yitzhaki, S., Olkin, I. (1991). Concentration indices and concentration curves, in K. Mosler and M. Scarsini (eds.), Stochastic Orders and Decisions under Risk, Institute of Mathematical Statistics: Lecture-Notes Monograph Series, 19, 1991, 380–392. [Google Scholar]) and Yitzhaki (2003 Yitzaki, S. (2003). Gini mean difference: A superior measure of variability for non normal distribution. Metron-International Journal of Statistics, LXI:285–316. [Google Scholar])), Modified rank correlation coefficient (cf. Zimmerman (1994 Zimmerman, D. W. (1994). A Note on modified rank correlation. Journal of educational and Behavioral Statistics 19:357–362. [Google Scholar])) and three modifications of Spearman rank correlation coefficient. We have observed that different forecasters do not necessarily offer same average performance. Moreover, an evidence of association between two criteria does not always lead us reaching at the same decision. The outcomes of the study may help the practitioners in selecting the best forecaster(s) for policymaking purposes.     

A Bayesian approach to analyse overdispersed longitudinal count data

In this paper, we consider a model for repeated count data, with within-subject correlation and/or overdispersion. It extends both the generalized linear mixed model and the negative-binomial model. This model, proposed in a likelihood context [17 G. Molenberghs, G. Verbeke, and C.G.B. Demétrio, An extended random-effects approach to modeling repeated, overdispersion count data, Lifetime Data Anal. 13 (2007), pp. 457–511.[Web of Science ®] , [Google Scholar],18 G. Molenberghs, G. Verbeke, C.G.B. Demétrio, and A. Vieira, A family of generalized linear models for repeated measures with normal and conjugate random effects, Statist. Sci. 25 (2010), pp. 325–347. doi: 10.1214/10-STS328[Crossref], [Web of Science ®] , [Google Scholar]] is placed in a Bayesian inferential framework. An important contribution takes the form of Bayesian model assessment based on pivotal quantities, rather than the often less adequate DIC. By means of a real biological data set, we also discuss some Bayesian model selection aspects, using a pivotal quantity proposed by Johnson [12 V.E. Johnson, Bayesian model assessment using pivotal quantities, Bayesian Anal. 2 (2007), pp. 719–734. doi: 10.1214/07-BA229[Crossref], [Web of Science ®] , [Google Scholar]].     

Improved Estimation of Finite Population Variance Using Auxiliary Information

This article addresses the problem of estimating of finite population variance using auxiliary information in simple random sampling. A ratio-cum-difference type class of estimators for population variance has been suggested with its properties under large sample approximation. It has been shown that the suggested class of estimators is more efficient than usual unbiased, difference, Das and Tripathi (1978 Das , A. K. , Tripathi , T. P. ( 1978 ). Use of auxiliary information in estimating the finite population variance . Sankhya C 40 : 139 – 148 . [Google Scholar]), Isaki (1983 Isaki , C. T. ( 1983 ). Variance estimation using auxiliary information . J. Amer. Statist. Assoc. 78 : 117 – 123 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), Singh et al. (1988 Singh , H. P. , Upadhyaya , L. N. , Namjoshi , U. D. ( 1988 ). Estimation of finite population variance . Curr. Sci. 57 : 1331 – 1334 .[Web of Science ®] , [Google Scholar]), Kadilar and Cingi (2006 Kadilar , C. , Cingi , H. ( 2006 ). Ratio estimators for the population variance in simple and stratified random sampling . Appl. Math. Comp. 173 ( 2 ): 1047 – 1059 .[Crossref], [Web of Science ®] , [Google Scholar]), and other estimators/classes of estimators. In addition, we support this theoretical result with the aid of a empirical study.     

On simulation of normal records

ABSTRACT

In the present paper, we discuss algorithms of record generation when records are taken from a normal population. We propose three new generation algorithms, compare their efficiency and find the most efficient algorithm (Algorithm 2.1). We then compare these algorithms with known generation algorithms presented in the work of Balakrishnan, So, and Zhu (2016 Balakrishnan, N., H. Y. So, and X. J. Zhu. 2016. On Box-Muller transformation and simulation of normal record data. Communication in Statistics – Simulation and Computations 45(10):3670–82.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]).     

A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study

The Significance Analysis of Microarrays (SAM; Tusher et al., 2001 Tusher , V. G. , Tibshirani , R. , Chu , G. ( 2001 ). Significance analysis of microarrys applied to the ionizing radiation response . Proceedings of the National Academy of Sciences 98 : 5116 – 5121 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) method is widely used in analyzing gene expression data while controlling the FDR by using resampling-based procedure in the microarray setting. One of the main components of the SAM procedure is the adjustment of the test statistic. The introduction of the fudge factor to the test statistic aims at deflating the large value of test statistics due to the small standard error of gene-expression. Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) pointed out that the fudge factor does not effectively improve the power and the control of the FDR as compared to the SAM procedure without the fudge factor in the presence of small variance genes. Motivated by the simulation results presented in Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), in this article, we extend our study to compare several methods for choosing the fudge factor in the modified t-type test statistics and use simulation studies to investigate the power and the control of the FDR of the considered methods.