Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis

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

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Comprehensive literature review and statistical considerations for microarray meta-analysis

(2012) George C. Tseng et al.   NUCLEIC ACIDS RESEARCH

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

(2011) Jesse M. Engreitz et al.   BIOINFORMATICS

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Content-based microarray search using differential expression profiles

(2011) Jesse M Engreitz et al.   BMC BIOINFORMATICS

Empirical comparison of cross-platform normalization methods for gene expression data

(2011) Jason Rudy et al.   BMC BIOINFORMATICS

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments

(2011) Robert R Kitchen et al.   BMC GENOMICS

Microarray-Based Class Discovery for Molecular Classification of Breast Cancer: Analysis of Interobserver Agreement

(2011) Alan Mackay et al.   JNCI-Journal of the National Cancer Institute

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles

(2010) Robert R Kitchen et al.   BMC GENOMICS

Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer

(2010) Vicky S. Sabine et al.   BREAST CANCER RESEARCH AND TREATMENT

Statistical aspects of quantitative real-time PCR experiment design

(2010) Robert R. Kitchen et al.   METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Consistency of predictive signature genes and classifiers generated using different microarray platforms

(2010) X Fan et al.   PHARMACOGENOMICS JOURNAL

Biomarkers of Dietary Energy Restriction in Women at Increased Risk of Breast Cancer

(2009) K. R. Ong et al.   Cancer Prevention Research

Confounding Effects in "A Six-Gene Signature Predicting Breast Cancer Lung Metastasis"

(2009) A. C. Culhane et al.   CANCER RESEARCH

Design and Optimization of Reverse-Transcription Quantitative PCR Experiments

(2009) A. Tichopad et al.   CLINICAL CHEMISTRY

Gene Expression Profiles Differentiating Between Breast Cancers Clinically Responsive or Resistant to Letrozole

(2009) William R. Miller et al.   JOURNAL OF CLINICAL ONCOLOGY

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Bioinformatics and breast cancer: what can high-throughput genomic approaches actually tell us?

(2009) A H Sims   JOURNAL OF CLINICAL PATHOLOGY

Cross-platform expression microarray performance in a mouse model of mitochondrial disease therapy

(2009) Zhe Zhang et al.   MOLECULAR GENETICS AND METABOLISM

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data

(2009) Nuno L. Barbosa-Morais et al.   NUCLEIC ACIDS RESEARCH

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

(2008) Andrew H Sims et al.   BMC Medical Genomics

Impact of Estrogen Deprivation on Gene Expression Profiles of Normal Postmenopausal Breast Tissue In vivo

(2008) A. Kendall et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION