1,305 research outputs found
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 s and 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
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