A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies

Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment

(2016) Roman Hornung et al.   BMC BIOINFORMATICS

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics

(2015) A. Sadanandam et al.   Cancer Discovery

Fast and Elegant Numerical Linear Algebra Using theRcppEigenPackage

(2015) Douglas Bates et al.   Journal of Statistical Software

Covariance adjustment for batch effect in gene expression data

(2014) Jung Ae Lee et al.   STATISTICS IN MEDICINE

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis

(2013) Sarah E. Reese et al.   BIOINFORMATICS

RcppArmadillo: Accelerating R with high-performance C++ linear algebra

(2013) Dirk Eddelbuettel et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

(2013) Anguraj Sadanandam et al.   NATURE MEDICINE

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

Genome-Wide Expression Analysis of Middle Eastern Colorectal Cancer Reveals FOXM1 as a Novel Target for Cancer Therapy

(2011) Shahab Uddin et al.   AMERICAN JOURNAL OF PATHOLOGY

Probabilistic principal component analysis for metabolomic data

(2011) Gift Nyamundanda et al.   BMC BIOINFORMATICS

A Cross-Species Analysis of a Mouse Model of Breast Cancer-Specific Osteolysis and Human Bone Metastases Using Gene Expression Profiling

(2011) Anguraj Sadanandam et al.   BMC CANCER

Molecular profiles and clinical outcome of stage UICC II colon cancer patients

(2011) Jörn Gröne et al.   INTERNATIONAL JOURNAL OF COLORECTAL DISEASE

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Intratumor Heterogeneity and Precision of Microarray-Based Predictors of Breast Cancer Biology and Clinical Outcome

(2010) William T. Barry et al.   JOURNAL OF CLINICAL ONCOLOGY

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

In vivo Antitumor Activity of MEK and Phosphatidylinositol 3-Kinase Inhibitors in Basal-Like Breast Cancer Models

(2009) K. P. Hoeflich et al.   CLINICAL CANCER RESEARCH

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

Quality Assessment for Short Oligonucleotide Microarray Data

(2008) Julia Brettschneider et al.   TECHNOMETRICS