R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish

Fermions and Kaluza-Klein vacuum decay: a toy model

We address the question of whether or not fermions with twisted periodicity condition suppress the semiclassical decay of M^4xS^1 Kaluza--Klein vacuum. We consider a toy (1+1)-dimensional model with twisted fermions in cigar-shaped Euclidean background geometry and calculate the fermion determinant. We find that contrary to expectations, the determinant is finite. We consider this as an indication that twisted fermions do not stabilize the Kaluza--Klein vacuum.Comment: 13 pages, 2 figure

Confinement in Covariant Gauges

We examine the weak coupling limit of Euclidean SU(n) gauge theory in covariant gauges. Following an earlier suggestion, an equivariant BRST-construction is used to define the continuum theory on a finite torus. The equivariant gauge fixing introduces constant ghost fields as moduli of the model. We study the parameter- and moduli- space perturbatively. For $n_f \leq n$ quark flavors, the moduli flow to a non-trivial fixed point in certain critical covariant gauges and the one-loop effective potential indicates that the global SU(n) color symmetry of the gauge fixed model is spontaneously broken to $U(1)^{n-1}$. Ward identities and renormalization group arguments imply that the longitudinal gauge boson propagator at long range is dominated by $n(n-1)$ Goldstone bosons in these critical covariant gauges. In the large $n$ limit, we derive a nonlinear integral equation for the expectation value of large Wilson loops assuming that the exchange of Goldstone bosons dominates the interaction at long range in critical covariant gauges. We find numerically that the expectation value of large circular Wilson loops decreases exponentially with the enclosed area in the absence of dynamical fermions. The gauge invariance of this mechanism for confinement in critical covariant gauges is discussed.Comment: 45 pages, Latex, uses psfig.sty and epsfig.sty to include postscript-figure

Mass Spectra of Supersymmetric Yang-Mills Theories in 1+1 Dimensions

Physical mass spectra of supersymmetric Yang-Mills theories in 1+1 dimensions are evaluated in the light-cone gauge with a compact spatial dimension. The supercharges are constructed and the infrared regularization is unambiguously prescribed for supercharges, instead of the light-cone Hamiltonian. This provides a manifestly supersymmetric infrared regularization for the discretized light-cone approach. By an exact diagonalization of the supercharge matrix between up to several hundred color singlet bound states, we find a rapidly increasing density of states as mass increases.Comment: LaTeX file, 32 page, 7 eps figure

On Zero Modes and the Vacuum Problem -- A Study of Scalar Adjoint Matter in Two-Dimensional Yang-Mills Theory via Light-Cone Quantisation

SU(2) Yang-Mills Theory coupled to massive adjoint scalar matter is studied in (1+1) dimensions using Discretised Light-Cone Quantisation. This theory can be obtained from pure Yang-Mills in 2+1 dimensions via dimensional reduction. On the light-cone, the vacuum structure of this theory is encoded in the dynamical zero mode of a gluon and a constrained mode of the scalar field. The latter satisfies a linear constraint, suggesting no nontrivial vacua in the present paradigm for symmetry breaking on the light-cone. I develop a diagrammatic method to solve the constraint equation. In the adiabatic approximation I compute the quantum mechanical potential governing the dynamical gauge mode. Due to a condensation of the lowest omentum modes of the dynamical gluons, a centrifugal barrier is generated in the adiabatic potential. In the present theory however, the barrier height appears too small to make any impact in this odel. Although the theory is superrenormalisable on naive powercounting grounds, the removal of ultraviolet divergences is nontrivial when the constrained mode is taken into account. The open aspects of this problem are discussed in detail.Comment: LaTeX file, 26 pages. 14 postscript figure

QED and String Theory

We analyze the D9-D9bar system in type IIB string theory using Dp-brane probes. It is shown that the world-volume theory of the probe Dp-brane contains two-dimensional and four-dimensional QED in the cases with p=1 and p=3, respectively, and some applications of the realization of these well-studied quantum field theories are discussed. In particular, the two-dimensional QED (the Schwinger model) is known to be a solvable theory and we can apply the powerful field theoretical techniques, such as bosonization, to study the D-brane dynamics. The tachyon field created by the D9-D9bar strings appears as the fermion mass term in the Schwinger model and the tachyon condensation is analyzed by using the bosonized description. In the T-dualized picture, we obtain the potential between a D0-brane and a D8-D8bar pair using the Schwinger model and we observe that it consists of the energy carried by fundamental strings created by the Hanany-Witten effect and the vacuum energy due to a cylinder diagram. The D0-brane is treated quantum mechanically as a particle trapped in the potential, which turns out to be a system of a harmonic oscillator. As another application, we obtain a matrix theory description of QED using Taylor's T-duality prescription, which is actually applicable to a wide variety of field theories including the realistic QCD. We show that the lattice gauge theory is naturally obtained by regularizing the matrix size to be finite.Comment: 33 pages, Latex, 4 figures, a reference adde

Tuning Fermilab Heavy Quarks in 2+1 Flavor Lattice QCD with Application to Hyperfine Splittings

We report the non-perturbative tuning of parameters--- kappa_c, kappa_b, and kappa_crit ---that determine the heavy-quark mass in the Fermilab action. This requires the computation of the masses of Ds^(*) and Bs^(*) mesons comprised of a Fermilab heavy quark and a staggered light quark. Additionally, we report the hyperfine splittings for Ds and Bs mesons as a cross-check of our simulation and analysis methods. We find a splitting of 145 +/- 15 MeV for the Ds system and 40 +/- 9 MeV for the Bs system. These are in good agreement with the Particle Data Group average values of 143.9 +/- 0.4 MeV and 46.1 +/- 1.5 MeV, respectively. The calculations are carried out with the MILC 2+1 flavor gauge configurations at three lattice spacings $a$ approximately 0.15, 0.12, and 0.09 fm.Comment: 34 pages, 8 figures, 26 tables; some sections rearranged for clarity; conclusions unchanged; version accepted by Phys. Rev.

Infrared Features of the Landau Gauge QCD

The infrared features of Landau gauge QCD are studied by the lattice simulation of $\beta=6.0, 16^4, 24^4, 32^4$ and $\beta=6.4, 32^4, 48^4$. We adopt two definitions of the gauge field; 1) $U-$linear 2) $\log U$ and measured the gluon propagator and ghost propagator. Infrared singularity of the gluon propagator is less than that of tree level result but the gluon propagator at 0 momentum remains finite. The infrared singularity of ghost propagator is stronger than the tree level. The QCD running coupling measured by using the gluon propagator and the ghost propagator has a maximum $\alpha_s(p)\simeq 1$ at around $p=0.5GeV$ and decreases as $p$ approaches 0. The data are analyzed in use of formula of the principle of minimal sensitivity(PMS), the effective charge method and the contour-improved perturbation method, which suggest necessity of the resummation of perturbation series in the infrared region together with existence of the infrared fixed point. Kugo-Ojima parameter saturates at about -0.8 in contrast to the theoretically expected value -1.Comment: RevTex4, 9 pages, 10 eps figures, Typos corrected. To be published in Phys. Rev. D(2004

Edge States and Entropy of 2d Black Holes

In several recent publications Carlip, as well as Balachandran, Chandar and Momen, have proposed a statistical mechanical interpretation for black hole entropy in terms of ``would be gauge'' degrees of freedom that become dynamical on the boundary to spacetime. After critically discussing several routes for deriving a boundary action, we examine their hypothesis in the context of generic 2-D dilaton gravity. We first calculate the corresponding statistical mechanical entropy of black holes in 1+1 deSitter gravity, which has a gauge theory formulation as a BF-theory. Then we generalize the method to dilaton gravity theories that do not have a (standard) gauge theory formulation. This is facilitated greatly by the Poisson-Sigma-model formulation of these theories. It turns out that the phase space of the boundary particles coincides precisely with a symplectic leaf of the Poisson manifold that enters as target space of the Sigma-model. Despite this qualitatively appealing picture, the quantitative results are discouraging: In most of the cases the symplectic leaves are non-compact and the number of microstates yields a meaningless infinity. In those cases where the particle phase space is compact - such as, e.g., in the Euclidean deSitter theory - the edge state degeneracy is finite, but generically it is far too small to account for the semiclassical Bekenstein-Hawking entropy.Comment: 36 pages, Late