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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Journal ArticleDOI
Apert p.Ser252Trp Mutation in FGFR2 Alters Osteogenic Potential and Gene Expression of Cranial Periosteal Cells
Roberto D. Fanganiello,Andréa L. Sertié,Eduardo M. Reis,Erika Yeh,Nélio A. J. Oliveira,Daniela Franco Bueno,Irina Kerkis,Nivaldo Alonso,Sergio Cavalheiro,Hamilton Matsushita,Renato da Silva Freitas,Sergio Verjovski-Almeida,Maria Rita Passos-Bueno +12 more
TL;DR: It is suggested that AS periosteal cells present enhanced osteogenic potential, and a set of novel genes involved in the pathophysiology of AS or other craniosynostotic conditions are identified.
Journal ArticleDOI
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events
TL;DR: It is shown that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
Journal ArticleDOI
When should one subtract background fluorescence in 2-color microarrays?
TL;DR: This paper uses simulation to systematically examine the bias-variance trade off of background subtraction under a variety of possible experimental conditions and identifies factors that are important for determining whether to background subtract, including the correlation of foreground to background intensity ratios.
Journal ArticleDOI
Hunting the primary: novel strategies for defining the origin of tumours.
Jayne L. Dennis,Karin A. Oien +1 more
TL;DR: The diagnostic problem of adenocarcinomas that present as metastases of unknown origin is reviewed, and it is demonstrated how integration of expression profiling techniques promises to throw new light on this important clinical challenge.
Journal ArticleDOI
Global gene expression analysis reveals specific and redundant roles for H1 variants, H1c and H10, in gene expression regulation
TL;DR: It is found that H1c and H1(0) act primarily as specific rather than global regulators of gene expression, which suggests that as well as having specific functions, the H1 variants share common roles in the organization of chromatin.
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