Estimating the Proportion of True Null Hypotheses for Multiple Comparisons

Whole genome microarray investigations (e.g. differential expression, differential methylation, ChIP-Chip) provide opportunities to test millions of features in a genome. Traditional multiple comparison procedures such as familywise error rate (FWER) controlling procedures are too conservative. Although false discovery rate (FDR) procedures have been suggested as having greater power, the control itself is not exact and depends on the proportion of true null hypotheses. Because this proportion is unknown, it has to be accurately (small bias, small variance) estimated, preferably using a simple calculation that can be made accessible to the general scientific community. We propose an easy-to-implement method and make the R code available, for estimating the proportion of true null hypotheses. This estimate has relatively small bias and small variance as demonstrated by (simulated and real data) comparing it with four existing procedures. Although presented here in the context of microarrays, this estimate is applicable for many multiple comparison situations

Trajectory and stability of Lagrangian point L2L_2 in the Sun-Earth system

This paper describes design of the trajectory and analysis of the stability of collinear point $L_2$ in the Sun-Earth system. The modified restricted three body problem with additional gravitational potential from the belt is used as the model for the Sun-Earth system. The effect of radiation pressure of the Sun and oblate shape of the Earth are considered. The point $L_2$ is asymptotically stable upto a specific value of time $t$ correspond to each set of values of parameters and initial conditions. The results obtained from this study would be applicable to locate a satellite, a telescope or a space station around the point $L_2$.Comment: Accepted for publication in Astrophysics & Space Scienc

Uniform random generation of large acyclic digraphs

Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory networks, not only the estimation of model parameters but the reconstruction of the structure itself is of great interest. As well as for the assessment of different structure learning algorithms in simulation studies, a uniform sample from the space of directed acyclic graphs is required to evaluate the prevalence of certain structural features. Here we analyse how to sample acyclic digraphs uniformly at random through recursive enumeration, an approach previously thought too computationally involved. Based on complexity considerations, we discuss in particular how the enumeration directly provides an exact method, which avoids the convergence issues of the alternative Markov chain methods and is actually computationally much faster. The limiting behaviour of the distribution of acyclic digraphs then allows us to sample arbitrarily large graphs. Building on the ideas of recursive enumeration based sampling we also introduce a novel hybrid Markov chain with much faster convergence than current alternatives while still being easy to adapt to various restrictions. Finally we discuss how to include such restrictions in the combinatorial enumeration and the new hybrid Markov chain method for efficient uniform sampling of the corresponding graphs.Comment: 15 pages, 2 figures. To appear in Statistics and Computin

Coexistence of ferro- and antiferromagnetic order in Mn-doped Ni2_2MnGa

Ni-Mn-Ga is interesting as a prototype of a magnetic shape-memory alloy showing large magnetic field induced strains. We present here results for the magnetic ordering of Mn-rich Ni-Mn-Ga alloys based on both experiments and theory. Experimental trends for the composition dependence of the magnetization are measured by a vibrating sample magnetometer (VSM) in magnetic fields of up to several tesla and at low temperatures. The saturation magnetization has a maximum near the stoichiometric composition and it decreases with increasing Mn content. This unexpected behaviour is interpreted via first-principles calculations within the density-functional theory. We show that extra Mn atoms are antiferromagnetically aligned to the other moments, which explains the dependence of the magnetization on composition. In addition, the effect of Mn doping on the stabilization of the structural phases and on the magnetic anisotropy energy is demonstrated.Comment: 4 pages, 3 figure

Periodic and Quasiperiodic Motion of an Elongated Microswimmer in Poiseuille Flow

We study the dynamics of a prolate spheroidal microswimmer in Poiseuille flow for different flow geometries. When moving between two parallel plates or in a cylindrical microchannel, the swimmer performs either periodic swinging or periodic tumbling motion. Although the trajectories of spherical and elongated swimmers are qualitatively similar, the swinging and tumbling frequency strongly depends on the aspect ratio of the swimmer. In channels with reduced symmetry the swimmers perform quasiperiodic motion which we demonstrate explicitely for swimming in a channel with elliptical cross section

Predicting the Amplitude of a Solar Cycle Using the North-South Asymmetry in the Previous Cycle: II. An Improved Prediction for Solar Cycle~24

Recently, using Greenwich and Solar Optical Observing Network sunspot group data during the period 1874-2006, (Javaraiah, MNRAS, 377, L34, 2007: Paper I), has found that: (1) the sum of the areas of the sunspot groups in 0-10 deg latitude interval of the Sun's northern hemisphere and in the time-interval of -1.35 year to +2.15 year from the time of the preceding minimum of a solar cycle n correlates well (corr. coeff. r=0.947) with the amplitude (maximum of the smoothed monthly sunspot number) of the next cycle n+1. (2) The sum of the areas of the spot groups in 0-10 deg latitude interval of the southern hemisphere and in the time-interval of 1.0 year to 1.75 year just after the time of the maximum of the cycle n correlates very well (r=0.966) with the amplitude of cycle n+1. Using these relations, (1) and (2), the values 112 + or - 13 and 74 + or -10, respectively, were predicted in Paper I for the amplitude of the upcoming cycle 24. Here we found that in case of (1), the north-south asymmetry in the area sum of a cycle n also has a relationship, say (3), with the amplitude of cycle n+1, which is similar to (1) but more statistically significant (r=0.968) like (2). By using (3) it is possible to predict the amplitude of a cycle with a better accuracy by about 13 years in advance, and we get 103 + or -10 for the amplitude of the upcoming cycle 24. However, we found a similar but a more statistically significant (r=0.983) relationship, say (4), by using the sum of the area sum used in (2) and the north-south difference used in (3). By using (4) it is possible to predict the amplitude of a cycle by about 9 years in advance with a high accuracy and we get 87 + or - 7 for the amplitude of cycle 24.Comment: 21 pages, 7 figures, Published in Solar Physics 252, 419-439 (2008

Recoil Polarization for Delta Excitation in Pion Electroproduction

We measured angular distributions of recoil-polarization response functions for neutral pion electroproduction for W=1.23 GeV at Q^2=1.0 (GeV/c)^2, obtaining 14 separated response functions plus 2 Rosenbluth combinations; of these, 12 have been observed for the first time. Dynamical models do not describe quantities governed by imaginary parts of interference products well, indicating the need for adjusting magnitudes and phases for nonresonant amplitudes. We performed a nearly model-independent multipole analysis and obtained values for Re(S1+/M1+)=-(6.84+/-0.15)% and Re(E1+/M1+)=-(2.91+/-0.19)% that are distinctly different from those from the traditional Legendre analysis based upon M1+ dominance and sp truncation.Comment: 5 pages, 2 figures, for PR

Population statistics study of radio and gamma-ray pulsars in the Galactic plane

We present results of our pulsar population synthesis of ordinary isolated and millisecond pulsars in the Galactic plane. Over the past several years, a program has been developed to simulate pulsar birth, evolution and emission using Monte Carlo techniques. We have added to the program the capability to simulate millisecond pulsars, which are old, recycled pulsars with extremely short periods. We model the spatial distribution of the simulated pulsars by assuming that they start with a random kick velocity and then evolve through the Galactic potential. We use a polar cap/slot gap model for $\gamma$-ray emission from both millisecond and ordinary pulsars. From our studies of radio pulsars that have clearly identifiable core and cone components, in which we fit the polarization sweep as well as the pulse profiles in order to constrain the viewing geometry, we develop a model describing the ratio of radio core-to-cone peak fluxes. In this model, short period pulsars are more cone-dominated than in our previous studies. We present the preliminary results of our recent study and the implications for observing these pulsars with GLAST and AGILE.Comment: 6 pages, 3 figures, 1 table, accepted in Astrophysics and Space Scienc