Eads B, Cash A, Bogart K, Costello J, Andrews J: Troubleshooting Microarray Hybridizations. Methods in Enzymology. 2006, 411: 34-49.
Article
CAS
PubMed
Google Scholar
Quackenbush J: Microarray data normalization and transformation. Nat Genet. 2002, 32 Suppl: 496-501. 10.1038/ng1032.
Article
PubMed
Google Scholar
Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucl Acids Res. 2001, 29: 2549-2557. 10.1093/nar/29.12.2549.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucl Acids Res. 2002, 30: e15-10.1093/nar/30.4.e15.
Article
PubMed Central
PubMed
Google Scholar
Grunenfelder B, Winzeler EA: Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet. 2002, 3: 653-661. 10.1038/nrg886.
Article
PubMed
Google Scholar
Tan PK, Downey TJ, Spitznagel EL, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucl Acids Res. 2003, 31: 5676-5684. 10.1093/nar/gkg763.
Article
CAS
PubMed Central
PubMed
Google Scholar
Miklos GLG, Maleszka R: Microarray reality checks in the context of a complex disease. Nat Biotech. 2004, 22: 615-621. 10.1038/nbt965.
Article
CAS
Google Scholar
Marshall E: Getting the Noise Out of Gene Arrays. Science. 2004, 306: 630-631. 10.1126/science.306.5696.630.
Article
CAS
PubMed
Google Scholar
Steinmetz LM, Davis RW: Maximizing the potential of functional genomics. Nat Rev Genet. 2004, 5: 190-201. 10.1038/nrg1293.
Article
CAS
PubMed
Google Scholar
Frantz S: An array of problems. Nat Rev Drug Discov. 2005, 4: 362-363. 10.1038/nrd1746.
Article
CAS
PubMed
Google Scholar
Michiels S, Koscielny S, Hill C: Prediction of cancer outcome with microarrays: a multiple random validation strategy. The Lancet. 2005, 365: 488-492. 10.1016/S0140-6736(05)17866-0.
Article
CAS
Google Scholar
Tibshirani R, Hong WJ, Warnke R, Chu G, Staudt LM, Wright G, Dave S: Immune Signatures in Follicular Lymphoma. N Engl J Med. 2005, 352: 1496-1497. 10.1056/NEJM200504073521422.
Article
CAS
PubMed
Google Scholar
Ein-Dor L, Zuk O, Domany E: Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. PNAS. 2006, 103: 5923-5928. 10.1073/pnas.0601231103.
Article
CAS
PubMed Central
PubMed
Google Scholar
Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES: Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics. 2005, 6: 63-10.1186/1471-2164-6-63.
Article
PubMed Central
PubMed
Google Scholar
Dobbin KK, Beer DG, Meyerson M, Yeatman TJ, Gerald WL, Jacobson JW, Conley B, Buetow KH, Heiskanen M, Simon RM, Minna JD, Girard L, Misek DE, Taylor JMG, Hanash S, Naoki K, Hayes DN, Ladd-Acosta C, Enkemann SA, Viale A, Giordano TJ: Interlaboratory Comparability Study of Cancer Gene Expression Analysis Using Oligonucleotide Microarrays. Clin Cancer Res. 2005, 11: 565-572.
CAS
PubMed
Google Scholar
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JGN, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005, 2: 345-350. 10.1038/nmeth756.
Article
CAS
PubMed
Google Scholar
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods. 2005, 2: 337-344. 10.1038/nmeth757.
Article
CAS
PubMed
Google Scholar
Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK: A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006, 24: 832-840. 10.1038/nbt1217.
Article
CAS
PubMed
Google Scholar
Shi L, Reid LH, Jones WD, MAQCconsortium: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006, 24: 1151-1161. 10.1038/nbt1239.
Article
CAS
PubMed
Google Scholar
Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM: Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotech. 2006, 24: 1115-1122. 10.1038/nbt1236.
Article
CAS
Google Scholar
Kluger Y, Yu H, Qian J, Gerstein M: Relationship between gene co-expression and probe localization on microarray slides. BMC Genomics. 2003, 4: 49-10.1186/1471-2164-4-49.
Article
PubMed Central
PubMed
Google Scholar
Balazsi G, Kay KA, Barabasi AL, Oltvai ZN: Spurious spatial periodicity of co-expression in microarray data due to printing design. Nucl Acids Res. 2003, 31: 4425-4433. 10.1093/nar/gkg485.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M: Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucl Acids Res. 2006, gkl871-
Google Scholar
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle. Molecular Cell. 1998, 2: 65-73. 10.1016/S1097-2765(00)80114-8.
Article
CAS
PubMed
Google Scholar
Cohen BA, Mitra RD, Hughes JD, Church GM: A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 2000, 26: 183-186. 10.1038/79896.
Article
CAS
PubMed
Google Scholar
Gottman JM: Time-series analysis: A comprehensive introduction for social scientists. New York: Cambridge University Press;. 1981
Google Scholar
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol Biol Cell. 1998, 9: 3273-3297.
Article
CAS
PubMed Central
PubMed
Google Scholar
Futschik ME, Crompton T: OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics. 2005, 21: 1724-1726. 10.1093/bioinformatics/bti199.
Article
CAS
PubMed
Google Scholar
Neuvial P, Hupe P, Brito I, Liva S, Manie E, Brennetot C, Radvanyi F, Aurias A, Barillot E: Spatial normalization of array-CGH data. BMC Bioinformatics. 2006, 7: 264-10.1186/1471-2105-7-264.
Article
PubMed Central
PubMed
Google Scholar
Reimers M, Weinstein JN: Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics. 2005, 6: 166-10.1186/1471-2105-6-166.
Article
PubMed Central
PubMed
Google Scholar
Bioconductor. [http://www.bioconductor.org]
Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ: Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet. 2000, 25: 333-337. 10.1038/77116.
Article
CAS
PubMed
Google Scholar
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD: Functional Discovery via a Compendium of Expression Profiles. Cell. 2000, 102: 109-126. 10.1016/S0092-8674(00)00015-5.
Article
CAS
PubMed
Google Scholar
Tirosh I, Weinberger A, Carmi M, Barkai N: A genetic signature of interspecies variations in gene expression. Nat Genet. 2006, 38: 830-834. 10.1038/ng1819.
Article
CAS
PubMed
Google Scholar
Naama Barkai lab Autocorrelations. [http://barkai-serv.weizmann.ac.il/autocorrelations/]
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N: Revealing modular organization in the yeast transcriptional network. Nat Genet. 2002, 31: 370-377.
CAS
PubMed
Google Scholar
Naama Barkai lab Modules. [http://www.weizmann.ac.il/home/jan/NG/MainFrames.html]
Stanford Microarray Database. [http://genome-www5.stanford.edu/]
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM: The Stanford Microarray Database. Nucl Acids Res. 2001, 29: 152-155. 10.1093/nar/29.1.152.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Science. 2002, 298: 799-804. 10.1126/science.1075090.
Article
CAS
PubMed
Google Scholar
Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998, 4: 1293-1301. 10.1038/3282.
Article
CAS
PubMed
Google Scholar
Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH: Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles. Science. 2000, 287: 873-880. 10.1126/science.287.5454.873.
Article
CAS
PubMed
Google Scholar
Saccharomyces Genome Database. [http://www.yeastgenome.org/]
Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL: Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. PNAS. 1999, 96: 14866-14870. 10.1073/pnas.96.26.14866.
Article
CAS
PubMed Central
PubMed
Google Scholar
Posas F, Chambers JR, Heyman JA, Hoeffler JP, de Nadal E, Arino J: The Transcriptional Response of Yeast to Saline Stress. J Biol Chem. 2000, 275: 17249-17255. 10.1074/jbc.M910016199.
Article
CAS
PubMed
Google Scholar
Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D: Characteristic genome rearrangements in experimental evolution of Saccharomycescerevisiae. PNAS. 2002, 99: 16144-16149. 10.1073/pnas.242624799.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dunn B, Levine RP, Sherlock G: Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. BMC Genomics. 2005, 6: 53-10.1186/1471-2164-6-53.
Article
PubMed Central
PubMed
Google Scholar