A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome

(2012) Isaac S. Kohane et al.   BIOINFORMATICS

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

(2012) M. N. McCall et al.   BIOINFORMATICS

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

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

The adult intestinal core microbiota is determined by analysis depth and health status

(2012) A. Salonen et al.   CLINICAL MICROBIOLOGY AND INFECTION

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

Making sense out of massive data by going beyond differential expression

(2012) P. R. Schmid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2011) Chao Chen et al.   PLoS One

Large scale comparison of global gene expression patterns in human and mouse

(2011) Xiangqun Zheng-Bradley et al.   GENOME BIOLOGY

Frozen robust multiarray analysis (fRMA)

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

Advanced Approaches to Characterize the Human Intestinal Microbiota by Computational Meta-analysis

(2010) Janne Nikkilä et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

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

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

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

(2009) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays

(2009) Leo Lahti et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

(2008) Sami Kilpinen et al.   GENOME BIOLOGY