- Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57, 289-300.
- Brooks, AN, Yang, L., Duff, MO, Hansen, KD, Park, JW, Dudoit, S., Brenner, SE, and Graveley, BR (2011). Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 21, 193-202.
- Buness, A., Huber, W., Steiner, K., Sültmann, H., and Poustka, A. (2005). arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics 21, 554-556.
- Callow, MJ, Dudoit, S., Gong, EL, Speed, TP, and Rubin, EM (2000). Microarray expression profiling identifies genes with altered expression in HDL deficient mice. Genome Research 10, 2022-2029.
- Carrel, L. and Willard, HF (2005). X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400-404.
- Chen, Y., Lun, ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438.
- Dalgaard, P. (2002). Introductory Statistics with R. Springer, New York.
- Diaz, E., Ge, Y., Yang, YH, Loh, KC, Serafini, TA, Okazaki, Y., Hayashizaki, Y., Speed, T., P., Ngai, J., and Scheiffele, P. (2002). Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron 36, 417-434.
- Durinck, S., Allemeersch, J., Carey, VJ, Moreau, Y., and De Moor, B. (2004). Importing MAGE-ML format microarray data into BioConductor. Bioinformatics 20, 3641-3642.
- Ellis, L., Pan, Y., Smyth, G., George, D., McCormack, C., Williams-Truax, R., Mita, M., Beck, J., Burris, H., Ryan, G., et al. (2008). Histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T-cell lymphoma. Clinical Cancer Research 14, 4500-4510.
- Hung, S., Baldi, P., and Hatfield, GW (2002). Global gene expression profiling in Escherichia coli K12: The effects of leucine-responsive regulatory protein. Journal of Biological Chemistry 277, 40309-40323.
- International HapMap Consortium, T. (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
- Irizarry, R. (2005). From CEL files to annotated lists of interesting genes. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions using R and Bioconductor, pages 431-442. Springer, New York.
- Law, CW, Alhamdoosh, M., Su, S., Smyth, GK, and Ritchie, ME (2016). RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5, 1408.
- Law, CW, Chen, Y., Shi, W., and Smyth, GK (2014). Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15, R29.
- Li, B. and Dewey, CN (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.
- Liao, Y., Smyth, GK, and Shi, W. (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research 41, e108.
- Liao, Y., Smyth, GK, and Shi, W. (2014). featureCounts: an efficient general-purpose read summarization program. Bioinformatics 30, 923-930.
- Lim, E., Vaillant, F., Wu, D., Forrest, N., Pal, B., Hart, A., Asselin-Labat, M., Gyorki, D., Ward, T., Partanen, A., et al. (2009). Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nature Medicine 15, 907-913.
- Linnaeus Centre for Bioinformatics, Uppsala University, S.
- Liu, R., Holik, AZ, Su, S., Jansz, N., Chen, K., Leong, HS, Blewitt, ME, Asselin-Labat, ML, Smyth, GK, and Ritchie, ME (2015). Why weight? modeling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research 43, e97.
- Milliken, GA and Johnson, DE (1992). Analysis of Messy Data, Volume 1: Designed Experiments. Chapman & Hall, New York.
- Morrissey, ER and Diaz-Uriarte, R. (2009). Pomelo II: finding differentially expressed genes. Nucleic Acids Research 37, W581-W586.
- Oshlack, A., Emslie, D., Corcoran, L., and Smyth, G. (2007). Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biology 8, R2.
- Peart, M., Smyth, G., Van Laar, R., Bowtell, D., Richon, V., Marks, P., Holloway, A., and Johnstone, R. (2005). Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proceedings of the National Academy of Sciences of the United States of America 102, 3697-3702.
- Phipson, B., Lee, S., Majewski, IJ, Alexander, WS, and Smyth, GK (2016). Robust hyper parameter estimation protects against hypervariable genes and improves power to detect differential expression. Annals of Applied Statistics 10, 946-963.
- Pickrell, JK, Marioni, JC, Pai, AA, Degner, JF, Engelhardt, BE, Nkadori, E., Veyrieras, JB, Stephens, M., Gilad, Y., and Pritchard, JK (2010). Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772.
- Pickrell, JK, Pai, AA, Gilad, Y., and Pritchard, JK (2010). Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genetics 6, e1001236.
- Rainer, J., Sanchez-Cabo, F., Stocker, G., Sturn, A., and Trajanoski, Z. (2006). CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis. Nucleic Acids Research 34, W498-503.
- Reiner, A., Yekutieli, D., and Benjamini, Y. (2003). Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19, 368-375.
- Ritchie, M., Diyagama, D., Neilson, J., Van Laar, R., Dobrovic, A., Holloway, A., and Smyth, G. (2006). Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics 7, 261.
- Ritchie, M., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23, 2700-2707.
- Ritchie, ME, Phipson, B., Wu, D., Hu, Y., Law, CW, Shi, W., and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47.
- Robinson, MD and Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11, R25.
- Royal Institute of Technology, Sweden (2005). KTH-package for microarray data analysis. Software package, http://www.biotech.kth.se/molbio/microarray/pages/kthpackagetransfer.html.
- Shi, W., De Graaf, C., Kinkel, S., Achtman, A., Baldwin, T., Schofield, L., Scott, H., Hilton, D., and Smyth, G. (2010). Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Research 38, 2168-2176.
- Shi, W., Oshlack, A., and Smyth, G. (2010). Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression Beadchips. Nucleic Acids Research 38, e204.
- Skaletsky, H., Kuroda-Kawaguchi, T., Minx, PJ, Cordum, HS, Hillier, L., Brown, LG, Repping, S., Pyntikova, T., Ali, J., Bieri, T., Chinwalla, A., Delehaunty, A., Delehaunty, K., Du, H., Fewell, G., Fulton, L., Fulton, R., Graves, T., Hou, SF, Latrielle, P., Leonard, S., Mardis, E., Maupin, R., McPherson, J., Miner, T., Nash, W., Nguyen, C., Ozersky, P., Pepin, K., Rock, S., Rohlfing, T., Scott, K., Schultz, B., Strong, C., Tin-Wollam, A., Yang, SP, Waterston, RH, Wilson, RK, Rozen, S., and Page, DC (2003). The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825-837.
- Smyth, G., Michaud, J., and Scott, H. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21, 2067-2075.
- Smyth, G. and Speed, T. (2003). Normalization of cDNA microarray data. Methods 31, 265-273.
- Smyth, G., Yang, Y., and Speed, T. (2003). Statistical issues in cDNA microarray data analysis. Methods in Molecular Biology 224, 111-136.
- Smyth, GK (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, Article 3.
- Smyth, GK and Altman, NS (2013). Separate-channel analysis of two-channel microarrays: recovering inter-spot information. BMC Bioinformatics 14, 165.
- Vaquerizas, JM, Dopazo, J., and Dıaz-Uriarte, R. (2004). DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics 20, 3656-3658.
- Visvader, JE (2009). Keeping abreast of the mammary epithelial hierarchy and breast tumorigenesis. Genes & development 23, 2563-2577.
- Weng, H. and Ayoubi, P. (2004). GPAP (GenePix Pro Auto-Processor) for online preprocessing, normalization and statistical analysis of primary microarray data. Software package, Microarray Core Facility, Oklahoma State University, http://darwin.biochem.okstate.edu/gpap3.
- Wettenhall, JM, Simpson, KM, Satterley, K., and Smyth, GK (2006). affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics 22, 897-899.
- Wettenhall, JM and Smyth, GK (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706.
- Wolfinger, RD, Gibson, G., Wolfinger, ED, Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., and Paules, RS (2001). Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology 8, 625-637.
- Wu, D., Lim, E., Vaillant, F., Asselin-Labat, M., Visvader, J., and Smyth, G. (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176-2182.
- Wu, D. and Smyth, G. (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133.
- Xia, X., McClelland, M., and Wang, Y. (2005). Webarray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306.
- Yang, YH, Dudoit, S., Luu, P., Lin, DM, Peng, V., Ngai, J., and Speed, TP (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30, e15.
- Yang, YH, Dudoit, S., Luu, P., and Speed, TP (2001). Normalization for cDNA microarray data. In ML Bittner, Y. Chen, AN Dorsel, and ER Dougherty, editors, Microarrays: Optical Technologies and Informatics, pages 141-152. Proceedings of SPIE, Volume 4266, San Jose, CA.
- Yang, YH and Speed, TP (2003). Design and analysis of comparative microarray experiments. In TP Speed, editor, Statistical Analysis of Gene Expression Microarray Data, pages 35-91. Chapman & Hall/CRC Press.
- Yang, YH and Thorne, NP (2003). Normalization for two-color cDNA microarray data. DR Goldstein, editor, Science and Statistics: A Festschrift for Terry Speed, pages 403-418. Institute of Mathematical Statistics Lecture Notes-Monograph Series, Volume 40.
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