Journal ArticleDOI
Microarray data normalization and transformation
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TLDR
This review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.Abstract:
Underlying every microarray experiment is an experimental question that one would like to address. Finding a useful and satisfactory answer relies on careful experimental design and the use of a variety of data-mining tools to explore the relationships between genes or reveal patterns of expression. While other sections of this issue deal with these lofty issues, this review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.read more
Citations
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Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex
TL;DR: Highly organized but only partly overlapping patterns of connectivity in MEG and fMRI functional networks are demonstrated, opening fundamentally new avenues for studying the relationship between cortical microarchitecture and multi-modal connectivity patterns.
Journal ArticleDOI
A Concentration-Dependent Analysis Method for High Density Protein Microarrays
TL;DR: A concentration-dependent analysis method is developed which normalizes protein microarray data based on the concentration of spotted probes, and it is shown that this analysis samples a data space that is complementary to other commonly employed analyses, and experimental validation of 92% of hits identified by the intersection of CDA with other tools.
Journal ArticleDOI
Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis
TL;DR: Evidence is provided that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes and RNA-Seq is used for improving draft genome annotations.
Journal ArticleDOI
Boron Accelerates Cultured Osteoblastic Cell Activity through Calcium Flux
Mark Luigi Fabian Capati,Ayako Nakazono,Kazunari Igawa,Kensuke Ookubo,Yuya Yamamoto,Kajirou Yanagiguchi,Shisei Kubo,Shizuka Yamada,Yoshihiko Hayashi +8 more
TL;DR: This is the first study to demonstrate the acceleration of Ca2+ flux by B supplementation in osteoblastic cells in vitro, related to the mechanism by which a very low concentration of B promotes the proliferation and differentiation of mammalian osteoblasts in vitro.
Journal ArticleDOI
Bootstrap method for the estimation of measurement uncertainty in spotted dual-color DNA microarrays.
TL;DR: A measurement-error model is presented that partitions the variance into general experimental sources and sources associated with the calculation of the ratio from noisy pixel data, described by a proportional (multiplicative) structure, while the latter is estimated using a statistical bootstrap method.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Book
Data Reduction and Error Analysis for the Physical Sciences
TL;DR: In this paper, Monte Carlo techniques are used to fit dependent and independent variables least squares fit to a polynomial least-squares fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Data Reduction and Error Analysis for the Physical Sciences.
TL;DR: Numerical methods matrices graphs and tables histograms and graphs computer routines in Pascal and Monte Carlo techniques dependent and independent variables least-squares fit to a polynomial least-square fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Robust Locally Weighted Regression and Smoothing Scatterplots
TL;DR: Robust locally weighted regression as discussed by the authors is a method for smoothing a scatterplot, in which the fitted value at z k is the value of a polynomial fit to the data using weighted least squares, where the weight for (x i, y i ) is large if x i is close to x k and small if it is not.
Book
Regression Analysis by Example
Samprit Chatterjee,B. Price +1 more
TL;DR: Simple linear regression Multiple linear regression Regression Diagnostics: Detection of Model Violations Qualitative Variables as Predictors Transformation of Variables Weighted Least Squares The Problem of Correlated Errors Analysis of Collinear Data Biased Estimation of Regression Coefficients Variable Selection Procedures Logistic Regression Appendix References as discussed by the authors