Stability and aggregation of ranked gene lists

Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature, but they have grown to a hot topic in the last few years, perhaps as a consequence of the increasing skepticism on the reproducibility and clinical applicability of molecular research findings. In this article, we review existing approaches for the assessment of stability of ranked gene lists and the related problem of aggregation, give some practical recommendations, and warn against potential misuse of these methods. This overview is illustrated through an application to a recent leukemia data set using the freely available Bioconductor package GeneSelector

Passive Scalar: Scaling Exponents and Realizability

An isotropic passive scalar field $T$ advected by a rapidly-varying velocity field is studied. The tail of the probability distribution $P(\theta,r)$ for the difference $\theta$ in $T$ across an inertial-range distance $r$ is found to be Gaussian. Scaling exponents of moments of $\theta$ increase as $\sqrt{n}$ or faster at large order $n$, if a mean dissipation conditioned on $\theta$ is a nondecreasing function of $|\theta|$. The $P(\theta,r)$ computed numerically under the so-called linear ansatz is found to be realizable. Some classes of gentle modifications of the linear ansatz are not realizable.Comment: Substantially revised to conform with published version. Revtex (4 pages) with 2 postscript figures. Send email to [email protected]

Universal statistics of non-linear energy transfer in turbulent models

A class of shell models for turbulent energy transfer at varying the inter-shell separation, $\lambda$, is investigated. Intermittent corrections in the continuous limit of infinitely close shells ($\lambda \rightarrow 1$) have been measured. Although the model becomes, in this limit, non-intermittent, we found universal aspects of the velocity statistics which can be interpreted in the framework of log-poisson distributions, as proposed by She and Waymire (1995, Phys. Rev. Lett. 74, 262). We suggest that non-universal aspects of intermittency can be adsorbed in the parameters describing statistics and properties of the most singular structure. On the other hand, universal aspects can be found by looking at corrections to the monofractal scaling of the most singular structure. Connections with similar results reported in other shell models investigations and in real turbulent flows are discussed.Comment: 4 pages, 2 figures available upon request to [email protected]

Lognormal scale invariant random measures

In this article, we consider the continuous analog of the celebrated Mandelbrot star equation with lognormal weights. Mandelbrot introduced this equation to characterize the law of multiplicative cascades. We show existence and uniqueness of measures satisfying the aforementioned continuous equation; these measures fall under the scope of the Gaussian multiplicative chaos theory developed by J.P. Kahane in 1985 (or possibly extensions of this theory). As a by product, we also obtain an explicit characterization of the covariance structure of these measures. We also prove that qualitative properties such as long-range independence or isotropy can be read off the equation.Comment: 31 pages; Probability Theory and Related Fields (2012) electronic versio

Periodically kicked turbulence

Periodically kicked turbulence is theoretically analyzed within a mean field theory. For large enough kicking strength A and kicking frequency f the Reynolds number grows exponentially and then runs into some saturation. The saturation level can be calculated analytically; different regimes can be observed. For large enough Re we find the saturation level to be proportional to A*f, but intermittency can modify this scaling law. We suggest an experimental realization of periodically kicked turbulence to study the different regimes we theoretically predict and thus to better understand the effect of forcing on fully developed turbulence.Comment: 4 pages, 3 figures. Phys. Rev. E., in pres

Generalized scaling in fully developed turbulence

In this paper we report numerical and experimental results on the scaling properties of the velocity turbulent fields in several flows. The limits of a new form of scaling, named Extended Self Similarity(ESS), are discussed. We show that, when a mean shear is absent, the self scaling exponents are universal and they do not depend on the specific flow (3D homogeneous turbulence, thermal convection , MHD). In contrast, ESS is not observed when a strong shear is present. We propose a generalized version of self scaling which extends down to the smallest resolvable scales even in cases where ESS is not present. This new scaling is checked in several laboratory and numerical experiment. A possible theoretical interpretation is also proposed. A synthetic turbulent signal having most of the properties of a real one has been generated.Comment: 25 pages, plain Latex, figures are available upon request to the authors ([email protected], [email protected]

A new scaling property of turbulent flows

We discuss a possible theoretical interpretation of the self scaling property of turbulent flows (Extended Self Similarity). Our interpretation predicts that, even in cases when ESS is not observed, a generalized self scaling, must be observed. This prediction is checked on a number of laboratory experiments and direct numerical simulations.Comment: Plain Latex, 1 figure available upon request to [email protected]

Longitudinal Structure Functions in Decaying and Forced Turbulence

In order to reliably compute the longitudinal structure functions in decaying and forced turbulence, local isotropy is examined with the aid of the isotropic expression of the incompressible conditions for the second and third order structure functions. Furthermore, the Karman-Howarth-Kolmogorov relation is investigated to examine the effects of external forcing and temporally decreasing of the second order structure function. On the basis of these investigations, the scaling range and exponents $\zeta_n$ of the longitudinal structure functions are determined for decaying and forced turbulence with the aid of the extended-self-similarity (ESS) method. We find that $\zeta_n$'s are smaller, for $n \geq 4$, in decaying turbulence than in forced turbulence. The reasons for this discrepancy are discussed. Analysis of the local slopes of the structure functions is used to justify the ESS method.Comment: 15 pages, 16 figure

Exact Resummations in the Theory of Hydrodynamic Turbulence: I The Ball of Locality and Normal Scaling

This paper is the first in a series of three papers that aim at understanding the scaling behaviour of hydrodynamic turbulence. We present in this paper a perturbative theory for the structure functions and the response functions of the hydrodynamic velocity field in real space and time. Starting from the Navier-Stokes equations (at high Reynolds number Re) we show that the standard perturbative expansions that suffer from infra-red divergences can be exactly resummed using the Belinicher-L'vov transformation. After this exact (partial) resummation it is proven that the resulting perturbation theory is free of divergences, both in large and in small spatial separations. The hydrodynamic response and the correlations have contributions that arise from mediated interactions which take place at some space- time coordinates. It is shown that the main contribution arises when these coordinates lie within a shell of a "ball of locality" that is defined and discussed. We argue that the real space-time formalism developed here offers a clear and intuitive understanding of every diagram in the theory, and of every element in the diagrams. One major consequence of this theory is that none of the familiar perturbative mechanisms may ruin the classical Kolmogorov (K41) scaling solution for the structure functions. Accordingly, corrections to the K41 solutions should be sought in nonperturbative effects. These effects are the subjects of papers II and III in this series, that will propose a mechanism for anomalous scaling in turbulence, which in particular allows multiscaling of the structure functions.Comment: PRE in press, 18 pages + 6 figures, REVTeX. The Eps files of figures will be FTPed by request to [email protected]

Variational bound on energy dissipation in plane Couette flow

We present numerical solutions to the extended Doering-Constantin variational principle for upper bounds on the energy dissipation rate in turbulent plane Couette flow. Using the compound matrix technique in order to reformulate this principle's spectral constraint, we derive a system of equations that is amenable to numerical treatment in the entire range from low to asymptotically high Reynolds numbers. Our variational bound exhibits a minimum at intermediate Reynolds numbers, and reproduces the Busse bound in the asymptotic regime. As a consequence of a bifurcation of the minimizing wavenumbers, there exist two length scales that determine the optimal upper bound: the effective width of the variational profile's boundary segments, and the extension of their flat interior part.Comment: 22 pages, RevTeX, 11 postscript figures are available as one uuencoded .tar.gz file from [email protected]