Affiliation: Brown University
- A review of statistical methods for preprocessing oligonucleotide microarraysZhijin Wu
Center for Statistical Sciences and Department of Community Health, Brown University, RI 02912, USA
Stat Methods Med Res 18:533-41. 2009..In this article, we review the issues encountered in each preprocessing step and introduce the statistical models and methods in preprocessing...
- Subset quantile normalization using negative control featuresZhijin Wu
Center for Statistical Sciences and Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
J Comput Biol 17:1385-95. 2010..It does not require an equal number of features in all samples and tolerates missing data...
- Quantitative assessment of hit detection and confirmation in single and duplicate high-throughput screeningsZhijin Wu
Center for Statistical Sciences, Department of Community Health, Brown University, Providence, RI 02903, USA
J Biomol Screen 13:159-67. 2008..However, false discovery rate based on empirically estimated null distribution is very close to observed false discovery proportion...
- Molecular alterations underlying the enhanced disruption of spermatogenesis by 2,5-hexanedione and carbendazim co-exposureSarah N Campion
Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
Reprod Toxicol 33:382-9. 2012..These findings provide candidate genes for further investigation of the testicular response to damage...
- Background adjustment for DNA microarrays using a database of microarray experimentsYunxia Sui
Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
J Comput Biol 16:1501-15. 2009..An R package dbRMA implementing our method can be obtained from the authors...
- Empirical bayes analysis of sequencing-based transcriptional profiling without replicatesZhijin Wu
Center for Statistical Sciences and Department of Community Health, Box G 121S 7, Brown University, Providence RI 02912, USA
BMC Bioinformatics 11:564. 2010..However, advances in technology do not remove biological variation between replicates and this variation is often neglected in many analyses...
- Suppression of radiation-induced testicular germ cell apoptosis by 2,5-hexanedione pretreatment. II. Gene array analysis reveals adaptive changes in cell cycle and cell death pathwaysSarah N Campion
Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
Toxicol Sci 117:457-65. 2010....
- Genetic variation in stearoyl-CoA desaturase 1 is associated with metabolic syndrome prevalence in Costa Rican adultsJian Gong
Department of Community Health, Brown University, Providence, RI, USA
J Nutr 141:2211-8. 2011..No gene-fatty acid interactive effects were observed. Our results suggest that genetic variation in the SCD1 gene may play a role in the development of MetS...
- Alternative statistical parameter for high-throughput screening assay quality assessmentYunxia Sui
Department of Community Health, Brown University, Providence, RI 02903, USA
J Biomol Screen 12:229-34. 2007..Studying the power of identifying true "hits" gives a more direct interpretation of assay quality and may provide guidance in assay optimization on some occasions...
- Exploration, visualization, and preprocessing of high-dimensional dataZhijin Wu
Center for Statistical Sciences, Brown University, Providence, RI, USA
Methods Mol Biol 620:267-84. 2010..In this chapter we review the common techniques in exploring and visualizing high-dimensional data and introduce the basic preprocessing procedures...
- Stochastic models inspired by hybridization theory for short oligonucleotide arraysZhijin Wu
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
J Comput Biol 12:882-93. 2005..We discuss how the proposed model can be used to obtain improved measures of expression useful for the data analysts...
- Comparison of Affymetrix GeneChip expression measuresRafael A Irizarry
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA
Bioinformatics 22:789-94. 2006..A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted...
- Feature-level exploration of a published Affymetrix GeneChip control datasetRafael A Irizarry
Genome Biol 7:404. 2006..A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16...
- A benchmark for Affymetrix GeneChip expression measuresLeslie M Cope
Department of Mathematical Sciences, Johns Hopkins University, 104 Whitehead Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
Bioinformatics 20:323-31. 2004..Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data...