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

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

(2011) J. Taminau et al.   BIOINFORMATICS

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

(2011) Jason Rudy et al.   BMC BIOINFORMATICS

Thawing Frozen Robust Multi-array Analysis (fRMA)

(2011) Matthew N McCall et al.   BMC BIOINFORMATICS

Batch effect correction for genome-wide methylation data with Illumina Infinium platform

(2011) Zhifu Sun et al.   BMC Medical Genomics

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

(2011) Chao Chen et al.   PLoS One

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

DSGeo: Software tools for cross-platform analysis of gene expression data in GEO

(2010) Ronilda Lacson et al.   JOURNAL OF BIOMEDICAL INFORMATICS

How to Deal with Batch Effect in Sequential Microarray Experiments?

(2010) Nino Demetrashvili  et al.   Molecular Informatics

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

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

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

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

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

WebArrayDB: cross-platform microarray data analysis and public data repository

(2009) Xiao-Qin Xia et al.   BIOINFORMATICS

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

(2008) Michael J Boedigheimer et al.   BMC GENOMICS

Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

(2008) Wynn L Walker et al.   BMC GENOMICS

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

Quality Assessment for Short Oligonucleotide Microarray Data

(2008) Julia Brettschneider et al.   TECHNOMETRICS