Home LiteratureArticle Details
PMID: 18718946 Published · ppublish English Journal Article

Eigen-R2 for dissecting variation in high-dimensional studies.

Bioinformatics (Oxford, England) ·Vol. 24 ·No. 19 ·2008-10-01 ·Pages 2260-2

Chen LS, Storey JD

Abstract

We provide a new statistical algorithm and software package called 'eigen-R(2)' for dissecting the variation of a high-dimensional biological dataset with respect to other measured variables of interest. We apply eigen-R(2) to two real-life examples and compare it with simply averaging R(2) over many features. An R-package eigenR2 is available at http://www.genomine.org/eigenr2/ and will be made publicly available via Bioconductor.

MeSH Terms
Algorithms Gene Expression Profiling Genetic Variation Models, Statistical Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Chen Lin S
Lewis-Sigler Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Storey John D
References (9)
9 references, click to expand
  1. Genetic dissection of transcriptional regulation in budding yeast.
    Science. 2002 Apr 26;296(5568):752-5 PMID: 11923494
  2. Genetic analysis of genome-wide variation in human gene expression.
    Nature. 2004 Aug 12;430(7001):743-7 PMID: 15269782
  3. Variation in gene expression within and among natural populations.
    Nat Genet. 2002 Oct;32(2):261-6 PMID: 12219088
  4. Singular value decomposition for genome-wide expression data processing and modeling.
    Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10101-6 PMID: 10963673
  5. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster.
    Nat Genet. 2001 Dec;29(4):389-95 PMID: 11726925
  6. Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 PMID: 11309499
  7. Capturing heterogeneity in gene expression studies by surrogate variable analysis.
    PLoS Genet. 2007 Sep;3(9):1724-35 PMID: 17907809
  8. Gene-expression variation within and among human populations.
    Am J Hum Genet. 2007 Mar;80(3):502-9 PMID: 17273971
  9. Systematic variation in gene expression patterns in human cancer cell lines.
    Nat Genet. 2000 Mar;24(3):227-35 PMID: 10700174
Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
Published
2008-10-01
Epub
2008-00-20
Pages
2260-2
Language
English
Region
England
NLM ID
9808944
PMCID
PMC4038975
Subset
IM
Grants
NHGRI NIH HHS · R01 HG002913 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com