quantro: a data-driven approach to guide the choice of an appropriate normalization method

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Statistical normalization techniques for magnetic resonance imaging

(2014) Russell T. Shinohara et al.   NeuroImage-Clinical

Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

(2013) Paul Yousefi et al.   Epigenetics

Blood-based profiles of DNA methylation predict the underlying distribution of cell types

(2013) Devin C Koestler et al.   Epigenetics

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Evaluating intensity normalization on MRIs of human brain with multiple sclerosis

(2010) Mohak Shah et al.   MEDICAL IMAGE ANALYSIS

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

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

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Making Informed Choices about Microarray Data Analysis

(2010) Mark Reimers   PLoS Computational Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Quantifying uncertainty in genotype calls

(2009) Benilton S. Carvalho et al.   BIOINFORMATICS

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS