Shambhala: a platform-agnostic data harmonizer for gene expression data

Gene‑gene interaction network analysis of hepatocellular carcinoma using bioinformatic software

(2018) Jin‑Hua He et al.   Oncology Letters

A semi-parametric statistical model for integrating gene expression profiles across different platforms

(2016) Yafei Lyu et al.   BMC BIOINFORMATICS

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

(2016) Joshua Xu et al.   Pharmaceutics

Seq-ing improved gene expression estimates from microarrays using machine learning

(2015) Paul K. Korir et al.   BMC BIOINFORMATICS

Sphericalk-Means Clustering

(2015) Kurt Hornik et al.   Journal of Statistical Software

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

PLIDA: cross-platform gene expression normalization using perturbed topic models

(2013) Amit G. Deshwar et al.   BIOINFORMATICS

Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis

(2013) Lifang Zhang et al.   BMC BIOINFORMATICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Cross-Platform Prediction of Gene Expression Signatures

(2013) Shu-Hong Lin et al.   PLoS One

R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment

(2012) Hanwen Huang et al.   BIOINFORMATICS

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

(2011) Jason Rudy et al.   BMC BIOINFORMATICS

Frozen robust multiarray analysis (fRMA)

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

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

(2010) Zhining Wen et al.   BMC BIOINFORMATICS

How to Deal with Batch Effect in Sequential Microarray Experiments?

(2010) Nino Demetrashvili  et al.   Molecular Informatics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

(2008) Seraya Maouche et al.   BMC GENOMICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE