Removing batch effects for prediction problems with frozen surrogate variable analysis

Batch effects are responsible for the failure of promising genomic prognos- tic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to re- move these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where sam- ples are analyzed one at a time for diagnostic, prognostic, and predictive applica- tions. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction ac- curacy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package

The tspair package for finding top scoring pair classifiers in R

Summary: Top scoring pairs (TSPs) are pairs of genes whose relative rankings can be used to accurately classify individuals into one of two classes. TSPs have two main advantages over many standard classifiers used in gene expression studies: (i) a TSP is based on only two genes, which leads to easily interpretable and inexpensive diagnostic tests and (ii) TSP classifiers are based on gene rankings, so they are more robust to variation in technical factors or normalization than classifiers based on expression levels of individual genes. Here I describe the R package, tspair, which can be used to quickly identify and assess TSP classifiers for gene expression data

Gene set bagging for estimating replicability of gene set analyses

Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach, called gene set bagging, for measuring the stability of ranking procedures using predefined gene sets. Gene set bagging involves resampling the original high-throughput data, performing gene-set analysis on the resampled data, and confirming that biological categories replicate. This procedure can be thought of as bootstrapping gene-set analysis and can be used to determine which are the most reproducible gene sets. Results: Here we apply this approach to two common genomics applications: gene expression and DNA methylation. Even with state-of-the-art statistical ranking procedures, significant categories in a gene set enrichment analysis may be unstable when subjected to resampling. Conclusions: We demonstrate that gene lists are not necessarily stable, and therefore additional steps like gene set bagging can improve biological inference of gene set analysis.Comment: 3 Figure

Characterization of a microwave frequency resonator via a nearby quantum dot

We present measurements of a hybrid system consisting of a microwave transmission-line resonator and a lateral quantum dot defined on a GaAs heterostructure. The two subsystems are separately characterized and their interaction is studied by monitoring the electrical conductance through the quantum dot. The presence of a strong microwave field in the resonator is found to reduce the resonant conductance through the quantum dot, and is attributed to electron heating and modulation of the dot potential. We use this interaction to demonstrate a measurement of the resonator transmission spectrum using the quantum dot.Comment: 3 pages, 3 figure

Double-sided coaxial circuit QED with out-of-plane wiring

Superconducting circuits are well established as a strong candidate platform for the development of quantum computing. In order to advance to a practically useful level, architectures are needed which combine arrays of many qubits with selective qubit control and readout, without compromising on coherence. Here we present a coaxial circuit QED architecture in which qubit and resonator are fabricated on opposing sides of a single chip, and control and readout wiring are provided by coaxial wiring running perpendicular to the chip plane. We present characterisation measurements of a fabricated device in good agreement with simulated parameters and demonstrating energy relaxation and dephasing times of $T_1 = 4.1\,\mu$s and $T_2 = 5.7\,\mu$s respectively. The architecture allows for scaling to large arrays of selectively controlled and measured qubits with the advantage of all wiring being out of the plane.Comment: 4 pages, 3 figures, 1 tabl