Normalization for triple-target microarray experiments

<p>Abstract</p> <p>Background</p> <p>Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are <it>Cy</it>3 and <it>Cy</it>5. Recent improvements in the technology (dye-labelling, scanner and, image analysis) allow hybridization up to four samples simultaneously. The two additional dyes are <it>Alexa</it>488 and <it>Alexa</it>494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data.</p> <p>Results</p> <p>We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize <it>p </it>differently labelled targets co-hybridized on a same array, for any value of <it>p </it>greater than 2.</p> <p>Conclusion</p> <p>The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.</p

New development in the CMS ECAL Level-1 trigger system to meet the challenges of LHC Run 2

International audienceAbstract - The CMS Electromagnetic Calorimeter (ECAL) provides energy sums to the Level-1Calorimeter Trigger at a rate of 40 MHz. The processing of these trigger primitives (TPs) isperformed by dedicated trigger concentrator cards (TCCs) located in the CMS service cavern.Updates to the functionality of the TCCs were required to respond to the challengingexperimental conditions of LHC Run 2, where the center-of-mass of proton-proton collisionenergy was 13 TeV and the peak instantaneous luminosity of the proton beams reached 2x1034cm$^{-2}$ s$^{-1}$. A new algorithm, termed the Cumulative Overflow Killing Engine (COKE), has beendeveloped and implemented via software and firmware updates to the TCCs in order toautomatically detect and mask noisy or problematic TPs via configurable thresholds. The autorecovery of the TCCs has also been improved, to manage the Single Event Upsets (SEUs) fromthe front-end electronics. This allows the detector to trigger efficiently without direct expertintervention, and the thresholds can evolve with evolving LHC conditions

Arabidopsis transcriptomics reveals conserved and divergent gene expression profiles between Arabidopsis thaliana accessions challenged with three different potyviruses

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ILD silicon tungsten electromagnetic calorimeter first full scale electronic prototype

International audienceThe “long slab” is a new prototype for the SiW-Ecal, a silicon tungsten electromagnetic calorimeter for the International Large Detector (ILD) at the future International Linear Collider (ILC). The new prototype has been evaluated with cosmics, radioactive sources and with 3 GeV electrons in beam tests at the DESY facility, Hamburg. A channel-wise calibration has been achieved, at different angles of incidence of the beam on the sensors. Using data collected at non-normal incidence, the signal of particles traversing adjacent pixels were used to estimate the absolute value of the trigger threshold in units of mips. This new prototype provides us many hints on how to improve the design of the front-end electronics. It is also a convenient tool to estimate the critical characteristics of ILD SiW-Ecal (like power consumption, cooling, readout time, etc.) and to optimise the future design of the detector

MPICH-V: Toward a Scalable Fault Tolerant MPI for Volatile Nodes

Global Computing platforms, large scale clusters and future TeraGRID systems gather thousands of nodes for computing parallel scientific applications. At this scale, node failures or disconnections are frequent events. This Volatility reduces the MTBF of the whole system in the range of hours or minutes