1,932 research outputs found
Spectral gene set enrichment (SGSE)
Motivation: Gene set testing is typically performed in a supervised context
to quantify the association between groups of genes and a clinical phenotype.
In many cases, however, a gene set-based interpretation of genomic data is
desired in the absence of a phenotype variable. Although methods exist for
unsupervised gene set testing, they predominantly compute enrichment relative
to clusters of the genomic variables with performance strongly dependent on the
clustering algorithm and number of clusters. Results: We propose a novel
method, spectral gene set enrichment (SGSE), for unsupervised competitive
testing of the association between gene sets and empirical data sources. SGSE
first computes the statistical association between gene sets and principal
components (PCs) using our principal component gene set enrichment (PCGSE)
method. The overall statistical association between each gene set and the
spectral structure of the data is then computed by combining the PC-level
p-values using the weighted Z-method with weights set to the PC variance scaled
by Tracey-Widom test p-values. Using simulated data, we show that the SGSE
algorithm can accurately recover spectral features from noisy data. To
illustrate the utility of our method on real data, we demonstrate the superior
performance of the SGSE method relative to standard cluster-based techniques
for testing the association between MSigDB gene sets and the variance structure
of microarray gene expression data. Availability:
http://cran.r-project.org/web/packages/PCGSE/index.html Contact:
[email protected] or [email protected]
Robert Frost Lecture at Bridgewater Teachers College
Length: 01:14:58
Robert Frost visited the Bridgewater Teachers College campus on December 1, 1959. That evening he gave a lecture for the campus community in the Horace Mann Auditorium. Frost spoke for over an hour, commenting on poetry and the teaching and appreciation of poetry. He recited and commented upon several of his own poems, including âAcquainted with the Night,â âDust of Snow,â âThe Tuft of Flowers,â âStopping by Woods on a Snowy Evening,â âThe Road Not Taken,â âOne More Brevity,â âMending Wall,â âA Leaf Treader,â âThe Night Light,â âThe Objection to Being Stepped On,â âDepartmental,â âAway!â and âA Considerable Speck.â
The recording abruptly stops during the sustained applause after Frost finished the lecture. The recording begins again in the middle of a sentence as Frost had resumed speaking after the applause.https://vc.bridgew.edu/media_sel/1011/thumbnail.jp
Principal component gene set enrichment (PCGSE)
Motivation: Although principal component analysis (PCA) is widely used for
the dimensional reduction of biomedical data, interpretation of PCA results
remains daunting. Most existing methods attempt to explain each principal
component (PC) in terms of a small number of variables by generating
approximate PCs with few non-zero loadings. Although useful when just a few
variables dominate the population PCs, these methods are often inadequate for
characterizing the PCs of high-dimensional genomic data. For genomic data,
reproducible and biologically meaningful PC interpretation requires methods
based on the combined signal of functionally related sets of genes. While gene
set testing methods have been widely used in supervised settings to quantify
the association of groups of genes with clinical outcomes, these methods have
seen only limited application for testing the enrichment of gene sets relative
to sample PCs. Results: We describe a novel approach, principal component gene
set enrichment (PCGSE), for computing the statistical association between gene
sets and the PCs of genomic data. The PCGSE method performs a two-stage
competitive gene set test using the correlation between each gene and each PC
as the gene-level test statistic with flexible choice of both the gene set test
statistic and the method used to compute the null distribution of the gene set
statistic. Using simulated data with simulated gene sets and real gene
expression data with curated gene sets, we demonstrate that biologically
meaningful and computationally efficient results can be obtained from a simple
parametric version of the PCGSE method that performs a correlation-adjusted
two-sample t-test between the gene-level test statistics for gene set members
and genes not in the set. Availability:
http://cran.r-project.org/web/packages/PCGSE/index.html Contact:
[email protected] or [email protected]
Social and Cultural Relations in the Grand Duchy of Lithuania. Microhistories, ed. by Richard Butterwick, Wioletta Pawlikowska, Routledge Research in Early Modern History, Routledge, New YorkâAbingdon, 2019, xii + 257 pp., 5 tables
Social and Cultural Relations in the Grand Duchy of Lithuania. Microhistories, ed. by Richard Butterwick, Wioletta Pawlikowska, Routledge Research in Early Modern History, Routledge, New YorkâAbingdon, 2019, xii + 257 pp., 5 table
Towards a History of Compromise : Comparing Political Unions in the British-Irish Isles and Poland-Lithuania
Acknowledgements I would like to thank the British Academy for inviting me to deliver the Raleigh Lecture, and Queenâs University Belfast for hosting the lecture despite the restrictions imposed during the Covid epidemic, and for the warmth of its welcome. Richard English was the perfect host and chair. Iâd like to thank all those in the audience, both in the hall and online, who asked such interesting and challenging questions. This expanded text owes much to their insights and probing of the issues. In particular, Iâd like to thank John Brewer, who first inspired me to think about compromise from the historianâs point of view, and Alvin Jackson for his pioneering comparative work on the Scottish and Irish unions, which provides much food for thought. I owe a great debt to Michael Brown, Colin Kidd, Michael Keating, and Sean Connolly, who read drafts of the text; they saved me from many infelicities, and their comments and suggestions were invaluable. Any infelicities that remain are entirely my responsibility.Peer reviewedPublisher PD
The Roads Not Taken : Liberty, Sovereignty and the Idea of the Republic in Poland-Lithuania and the British Isles, 1550â1660
Peer reviewedPostprin
Fraser River Gold Rush Adventures
"I submit to you my personal recollections of an overland trip from the Dalles, Oregon, to the Fraser River mines in 1858, which includes the fight the McLaughlin party had with the Indians, in what is now known as McLaughlin Canyon on the Okanogan River.
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