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Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

Witten, Daniela; Tibshirani, Robert - In: Statistical Applications in Genetics and Molecular Biology 8 (2009) 1, pp. 28-28

In recent work, several authors have introduced methods for sparse canonical correlation analysis (sparse CCA). Suppose that two sets of measurements are available on the same set of observations. Sparse CCA is a method for identifying sparse linear combinations of the two sets of variables that...

Persistent link: https://www.econbiz.de/10005046571

Visualisation of Gene Expression Data Ã¢ÂÂ the GE-biplot, the Chip-plot and the Gene-plot

Pittelkow, Yvonne; Wilson, Susan - In: Statistical Applications in Genetics and Molecular Biology 2 (2007) 1, pp. 6-6

Visualisation methods for exploring microarray data are particularly important for gaining insight into data from gene …. Further, good visualisation techniques are useful for outlier detection in microarray data and for aiding biological … display of microarray data as both the genes and the chips can be simultaneously plotted. In this paper we describe several …

Persistent link: https://www.econbiz.de/10005046577

Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels

Ingrid LÃÂ¶nnstedt; Rimini, Rebecca; Nilsson, Peter - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 7-7

research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few …

Persistent link: https://www.econbiz.de/10005046615

Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies

Jaeger, Jochen; Weichenhan, Dieter; Ivandic, Boris; … - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 9-9

We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a small number of individual patient samples. From this Phase-1 data a panel of marker genes is...

Persistent link: https://www.econbiz.de/10005046621

Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs

Ogorek, Benjamin; Stefanski, Leonard - In: Statistical Applications in Genetics and Molecular Biology 8 (2009) 1, pp. 2-2

There is great interest in finding human genes expressed through pharmaceutical intervention, thus opening a genomic window into benefit and side-effect profiles of a drug. Human insight gained from FDA-required animal experiments has historically been limited, but in the case of gene expression...

Persistent link: https://www.econbiz.de/10005585054

Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities

Jorge GarcÃÂa de la Nava; Hijum, Sacha van; … - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 11-11

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is...

Persistent link: https://www.econbiz.de/10005585060

Data Distribution of Short Oligonucleotide Expression Arrays and Its Application to the Construction of a Generalized Intellectual Framework

Konishi, Tomokazu - In: Statistical Applications in Genetics and Molecular Biology 7 (2008) 1, pp. 25-25

Information obtained by microarray studies frequently cause discrepancies between projects, laboratories and/or even …

Persistent link: https://www.econbiz.de/10005585064

Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject

Heller, Glenn; Qin, Jing - In: Statistical Applications in Genetics and Molecular Biology 6 (2007) 1, pp. 14-14

An objective of microarray data analysis is to identify gene expressions that are associated with a disease related …

Persistent link: https://www.econbiz.de/10005585087

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data

JÃÂ¶rg RahnenfÃÂ¼hrer; Domingues, Francisco; … - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 16-16

findings from microarray experiments.Recently introduced methods test if members of predefined gene sets are enriched in a list … of top-ranked genes in a microarray study. We improve this approach by defining scores that depend on all members of the …

Persistent link: https://www.econbiz.de/10005585090

Fully Bayesian Mixture Model for Differential Gene Expression: Simulations and Model Checks

Lewin, Alex; Bochkina, Natalia; Richardson, Sylvia - In: Statistical Applications in Genetics and Molecular Biology 6 (2007) 1, pp. 36-36

We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially...

Persistent link: https://www.econbiz.de/10005585098