Skip to main content
Grant Details

Grant Number: 5R01CA151947-02 Interpret this number
Primary Investigator: Qin, Li-Xuan
Organization: Sloan-Kettering Inst Can Research
Project Title: Statistical Methods for Normalizing Microarrays in Cancer Biomarker Studies
Fiscal Year: 2012
Back to top


DESCRIPTION (provided by applicant): Various array normalization methods have been developed for gene expression microarrays. Most of these methods assume few or symmetric differential expression between sample groups. There has been no systematic study of the properties of these methods in normalizing microRNA expression arrays utilizing heterogeneous samples such as tumors. MicroRNA arrays contain only a few hundred microRNAs, and are likely to have a relatively large proportion being differentially expressed between diverse tumor groups. The assessment of normalization methods in this setting is difficult because of the lack of a benchmark dataset that has no confounding array effects. We propose to design and generate such benchmark datasets, perform a systematic assessment of normalization methods with a particular emphasis on the utility of these models for detecting markers with differential expression, and from the benchmark data design derive statistical models that acknowledge heterogeneities inherent to tumor samples. PUBLIC HEALTH RELEVANCE: Microarrays are being widely used in cancer research. A critical step for processing microarray data is to normalize the arrays so that measurements from different arrays are comparable. There is a great need to evaluate the properties of statistical methods for array normalization when they are applied to microRNA arrays utilizing heterogeneous samples such as tumors.

Back to top


Cautionary Note on Using Cross-Validation for Molecular Classification.
Authors: Qin L.X. , Huang H.C. , Begg C.B. .
Source: Journal Of Clinical Oncology : Official Journal Of The American Society Of Clinical Oncology, 2016-09-06 00:00:00.0; , .
EPub date: 2016-09-06 00:00:00.0.
PMID: 27601553
Related Citations

Study Design And Data Analysis Considerations For The Discovery Of Prognostic Molecular Biomarkers: Acase Studyofprogression Free Survival In Advanced Serous Ovarian Cancer
Authors: Qin L.X. , Levine D.A. .
Source: Bmc Medical Genomics, 2016-06-10 00:00:00.0; 9(1), p. 27.
PMID: 27282150
Related Citations

Empirical Insights Into The Stochasticity Of Small Rna Sequencing
Authors: Qin L.X. , Tuschl T. , Singer S. .
Source: Scientific Reports, 2016; 6, p. 24061.
PMID: 27052356
Related Citations

Molecular Subtypes Of Uterine Leiomyosarcoma And Correlation With Clinical Outcome
Authors: Barlin J.N. , Zhou Q.C. , Leitao M.M. , Bisogna M. , Olvera N. , Shih K.K. , Jacobsen A. , Schultz N. , Tap W.D. , Hensley M.L. , et al. .
Source: Neoplasia (new York, N.y.), 2015 Feb; 17(2), p. 183-9.
PMID: 25748237
Related Citations

Differential Expression Analysis For Rna-seq: An Overview Of Statistical Methods And Computational Software
Authors: Huang H.C. , Niu Y. , Qin L.X. .
Source: Cancer Informatics, 2015; 14(Suppl 1), p. 57-67.
PMID: 26688660
Related Citations

Blocking And Randomization To Improve Molecular Biomarker Discovery
Authors: Qin L.X. , Zhou Q. , Bogomolniy F. , Villafania L. , Olvera N. , Cavatore M. , Satagopan J.M. , Begg C.B. , Levine D.A. .
Source: Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research, 2014-07-01 00:00:00.0; 20(13), p. 3371-8.
PMID: 24788100
Related Citations

Finding Gene Clusters For A Replicated Time Course Study
Authors: Qin L.X. , Breeden L. , Self S.G. .
Source: Bmc Research Notes, 2014; 7, p. 60.
PMID: 24460656
Related Citations

Microrna Array Normalization: An Evaluation Using A Randomized Dataset As The Benchmark
Authors: Qin L.X. , Zhou Q. .
Source: Plos One, 2014; 9(6), p. e98879.
PMID: 24905456
Related Citations

Corm: An R Package Implementing The Clustering Of Regression Models Method For Gene Clustering
Authors: Shi J. , Qin L.X. .
Source: Cancer Informatics, 2014; 13(Suppl 4), p. 11-3.
PMID: 25452684
Related Citations

Preprocessing Steps For Agilent Microrna Arrays: Does The Order Matter?
Authors: Qin L.X. , Huang H.C. , Zhou Q. .
Source: Cancer Informatics, 2014; 13(Suppl 4), p. 105-9.
PMID: 26380547
Related Citations

An Empirical Evaluation Of Normalization Methods For Microrna Arrays In A Liposarcoma Study
Authors: Qin L.X. , Tuschl T. , Singer S. .
Source: Cancer Informatics, 2013; 12, p. 83-101.
PMID: 23589668
Related Citations

Back to Top