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タグ: affymetrix [144 articles]

Recent papers classified by the tag affymetrix.
  • Pre-filtering improves reliability of Affymetrix GeneChips results when used to analyze gene expression in complex tissues.
    Mol Cell Probes (28 November 2007)
    by Dario Greco, Damiana Leo, Umberto di Porzio, Carla Perrone Capano, Petri Auvinen
    posted to affymetrix analysis microarray by yevishere on 2008-01-04 00:34:49 as ** along with 1 person Terkko
  • Effects of filtering by Present call on analysis of microarray experiments.
    BMC Bioinformatics, Vol. 7 (2006)
    by JN McClintick, HJ Edenberg
    posted to affymetrix analysis filtering by yevishere on 2008-01-04 00:35:46 as **** along with 2 people ghattem waszak
  • An overview of image-processing methods for Affymetrix GeneChips.
    Brief Bioinform (5 December 2007)
    by Jose M M Arteaga-Salas, Harry Zuzan, William B B Langdon, Graham J G J Upton, Andrew P P Harrison
    posted to affymetrix analysis by yevishere on 2008-01-04 00:33:28 as ** along with 3 people jyuh jfr aswin
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816.
    posted to affymetrix encode genomics race by xingxu on 2007-08-01 21:32:45 as read along with 24 people and 3 groups pengchy raistrick jyuh cmmorel dpollard ilh djkt plofje ramensky joepickrell massivemayhem fishtank Garamonfok jmuhlich bioyang cabbagezs antonkratz mimulus_99 julianjonker gjuggler drbal maralena ep161302 jasonflannick Bioinformatics EisenLab SorgerLab
  • notes Biological function of unannotated transcription during the early development of Drosophila melanogaster
    Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158.
    by Robert J Manak, Sujit Dike, Victor Sementchenko, Philipp Kapranov, Frederic Biemar, Jeff Long, Jill Cheng, Ian Bell, Srinka Ghosh, Antonio Piccolboni, Thomas R Gingeras
    posted to affymetrix drosophila genomics race by xingxu on 2007-08-01 22:01:48 as read along with 7 people and 6 groups GeeSharpMinor emptyhb dpollard neveaire djkt wrowell Stew Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience Cline_lab
  • Summaries of Affymetrix GeneChip probe level data.
    Nucleic Acids Res, Vol. 31, No. 4. (15 February 2003)
    by RA Irizarry, BM Bolstad, F Collin, LM Cope, B Hobbs, TP Speed
    posted to affymetrix genechipsummaries by wirawan on 2008-03-12 10:47:04 as ** along with 11 people pcahan1 RMGraze aviad_work vplagnol ghattem talponer heliopais waszak rschulz bertelsen srp33
  • An application for assessing quality of RNA hybridized to Affymetrix GeneChips.
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2699-2701.
    by KJ Archer, T Guennel
    posted to affymetrix microarray qc statistics by waszak on 2007-11-13 20:12:18 as ** along with 2 people jfr ghattem
  • Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality.
    J Biotechnol, Vol. 127, No. 4. (20 January 2007), pp. 549-559.
    by V Copois, F Bibeau, C Bascoul-Mollevi, N Salvetat, P Chalbos, C Bareil, L Candeil, C Fraslon, E Conseiller, V Granci, P Mazière, A Kramar, M Ychou, B Pau, P Martineau, F Molina, M Del Rio
    posted to affymetrix microarray qc by waszak on 2007-11-13 20:14:04 as ** along with 3 people jfr ghattem bertelsen
  • Explaining differences in saturation levels for Affymetrix GeneChip(R) arrays.
    Nucleic Acids Res (12 June 2007)
    by Dmitriy Skvortsov, Diana Abdueva, Christina Curtis, Betty Schaub, Simon Tavaré
    posted to affymetrix microarray by waszak on 2007-11-13 20:05:20 as ** along with 6 people jfr gpalidwor sebastien_vigneau ghattem ptrobajo bertelsen
  • Filtering genes to improve sensitivity in oligonucleotide microarray data analysis.
    Nucleic Acids Res (15 August 2007)
    by Stefano Calza, Wolfgang Raffelsberger, Alexander Ploner, Jose Sahel, Thierry Leveillard, Yudi Pawitan
    posted to affymetrix normalization by waszak on 2007-12-03 20:18:23 as ** along with 6 people frohike jyuh jfr rdiaz niallhaslam laral
  • oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
    Bioinformatics (17 September 2007), btm469.
    by Remo Sanges, Francesca Cordero, Raffaele A Calogero
    posted to affymetrix bioconductor r software by waszak on 2007-12-10 14:27:34 as ** along with 2 people jyuh rdiaz
  • Microarray Blob-Defect Removal Improves Array Analysis.
    Bioinformatics (1 March 2007)
    by Jun S S Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X Shirley Liu
    posted to affymetrix microarray software tiling by waszak on 2007-11-13 20:57:22 as ** along with 5 people and 1 group jfr kengg shigepong ghattem caseybrown Plantandetc
  • Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes.
    BMC Syst Biol, Vol. 1 (2007)
    by PR Bushel, RD Wolfinger, G Gibson
    posted to affymetrix microarray software by waszak on 2007-11-14 11:00:55 as ** along with 1 person jfr
  • Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array
    BMC Genomics, Vol. 7 (27 December 2006), 325.
    by Paul J Gardina, Tyson A Clark, Brian Shimada, Michelle K Staples, Qing Yang, James Veitch, Anthony Schweitzer, Tarif Awad, Charles Sugnet, Suzanne Dee, Christopher Davies, Alan Williams, Yaron Turpaz
    posted to affymetrix cancer colon exon splicing by waszak on 2008-01-30 14:04:56 as ** along with 2 people jfr srp33
  • How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results.
    BMC Bioinformatics, Vol. 7 (2006)
    by FF Millenaar, J Okyere, ST May, M van Zanten, LA Voesenek, AJ Peeters
    posted to affymetrix microarray statistics by waszak on 2007-11-13 20:56:03 as ** along with 6 people GeeSharpMinor gabe_rosser jfr neveaire ghattem pure39
  • Probe selection and expression index computation of affymetrix exon arrays.
    PLoS ONE, Vol. 1 (2006)
    by Y Xing, K Kapur, WH Wong
    posted to affymetrix algorithm huex hugene by waszak on 2008-08-15 15:50:05 as ** along with 1 person jfr
  • Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments
    Nucl. Acids Res., Vol. 36, No. 13. (1 August 2008), pp. 4417-4423.
    by David Benovoy, Tony Kwan, Jacek Majewski
    posted to snp microarray exon csh affymetrix by waszak on 2008-10-07 22:40:50 as ** along with 3 people jfr GeeSharpMinor caseybrown
  • RReportGenerator : Automatic reports from routine statistical analysis using R
    Bioinformatics (24 November 2007), btm556.
    by Wolfgang Raffelsberger, Yannick Krause, Luc Moulinier, David Kieffer, Anne-Laure Morand, Laurent Brino, Olivier Poch
    posted to affymetrix r by waszak on 2007-12-03 20:39:09 as ** along with 7 people natstreet druvus jyuh jfr mailund maralena GeeSharpMinor
  • A robust statistical method for case-control association testing with copy number variation.
    Nature genetics (7 September 2008)
    by Chris Barnes, Vincent Plagnol, Tomas Fitzgerald, Richard Redon, Jonathan Marchini, David Clayton, Matthew E E Hurles
    posted to software snp r ld gmm em cnv associationstudy algorithm affymetrix by waszak on 2008-10-08 15:01:08 as ** along with 9 people and 1 group caseybrown Zephyrus dakelley buyske misonneh djkt rdiaz Stew jyuh Roswell Cancer Crosstalk
  • RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.
    Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2825-2827.
    by F Hong, R Breitling, CW McEntee, BS Wittner, JL Nemhauser, J Chory
    posted to affymetrix bioconductor microarray software by waszak on 2007-11-13 21:43:39 as *** along with 2 people jfr sanchezbuelna
  • CoXpress: differential co-expression in gene expression data
    BMC Bioinformatics, Vol. 7 (20 November 2006), 509.
    by Michael Watson
    posted to affymetrix co-expression microarray networks software statistics by waszak on 2007-11-13 21:28:58 as ***** along with 5 people jfr dquest shigepong dps gabe_rosser
  • Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA
    BMC Biotechnology, Vol. 7 (13 September 2007), 57.
    by Karol L Thompson, Scott P Pine, Barry A Rosenzweig, Yaron Turpaz, Jacques Retief
    posted to affymetrix microarray quality rna by waszak on 2008-01-30 14:02:28 as ** along with 2 people jfr caseybrown
  • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset.
    Genome Biol, Vol. 6, No. 2. (2005)
    by SE Choe, M Boutros, AM Michelson, GM Church, MS Halfon
    posted to affymetrix analysis genechip methodology by waszak on 2008-01-30 14:59:12 as ** along with 5 people and 1 group xwbcn jeremymiller ccr ghattem daforerog GeschwindLab
  • Normalization of oligonucleotide arrays based on the least-variant set of genes
    BMC Bioinformatics, Vol. 9 (05 March 2008), 140.
    by Stefano Calza, Davide Valentini, Yudi Pawitan
    posted to affymetrix algorithm normalization by waszak on 2008-03-07 09:32:06 as ** along with 4 people jyuh jfr giovenko GeeSharpMinor
  • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. e175-e175.
    by Manhong Dai, Pinglang Wang, Andrew D Boyd, Georgi Kostov, Brian Athey, Edward G Jones, William E Bunney, Richard M Myers, Terry P Speed, Huda Akil, Stanley J Watson, Fan Meng
    posted to affymetrix genechip microarray by waszak on 2008-08-16 01:09:07 as ** along with 9 people and 2 groups giovenko pcahan1 frohike incovoma nicholso heliopais Montrachet shikin bertelsen Bioinformatics GeneGo
  • The utility of MAS5 expression summary and detection call algorithms
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Stuart Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller
    posted to affymetrix algorithm normalization by waszak on 2007-12-03 21:08:03 as ** along with 4 people heliopais jfr ryanraaum wirawan
  • Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis
    Mol Cell Proteomics (18 March 2008), M700590-MCP200.
    by Kasper Thorsen, Karina D Sorensen, Anne S Brems-Eskildsen, Charlotte Modin, Mette Gaustadnes, Anne-Mette K Hein, Mogens Kruhoffer, Soren Laurberg, Michael Borre, Kai Wang, Soren Brunak, Adrian R Krainer, Niels Torring, Lars Dyrskjot, Claus L Andersen, Torben F Orntoft
    posted to affymetrix cancer hugene splicing by waszak on 2008-04-10 16:54:10 as ** along with 2 people jo_davies jfr
  • Evaluation of quality-control criteria for microarray gene expression analysis.
    Clin Chem, Vol. 50, No. 11. (November 2004), pp. 1994-2002.
    by CI Dumur, S Nasim, AM Best, KJ Archer, AC Ladd, VR Mas, DS Wilkinson, CT Garrett, A Ferreira-Gonzalez
    posted to affymetrix microarray qc by waszak on 2007-11-13 20:08:06 as ** along with 1 person ghattem
  • Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
    Genome Res., Vol. 16, No. 12. (1 December 2006), pp. 1575-1584.
    by Daisuke Komura, Fan Shen, Shumpei Ishikawa, Karen R Fitch, Wenwei Chen, Jane Zhang, Guoying Liu, Sigeo Ihara, Hiroshi Nakamura, Matthew E Hurles, Charles Lee, Stephen W Scherer, Keith W Jones, Michael H Shapero, Jing Huang, Hiroyuki Aburatani
    posted to snp microarray human genome cnv algorithm affymetrix by waszak on 2008-10-08 14:40:40 as ** along with 8 people and 4 groups jfr dchughes giovanni jeremymiller frohike vpschulz shigepong debasis Bioinformatics G4ID GeschwindLab Genetics-of-Gambling
  • A comparison of Affymetrix gene expression arrays
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Mark Robinson, Terence Speed
    posted to affymetrix exon huex hugene by waszak on 2008-01-30 14:06:16 as ** along with 2 people jfr hpaces
  • GGtools: analysis of genetics of gene expression in bioconductor.
    Bioinformatics, Vol. 23, No. 4. (15 February 2007), pp. 522-523.
    by VJ Carey, M Morgan, S Falcon, R Lazarus, R Gentleman
    posted to affymetrix bioconductor microarray software by waszak on 2007-11-13 21:12:54 as ** along with 3 people jyuh jfr sanchezbuelna
  • Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Leah Mechanic, Brian Luke, Julie Goodman, Stephen Chanock, Curtis Harris
    posted to affymetrix algorithm snps by waszak on 2008-03-07 09:32:25 as ** along with 2 people jyuh omalbam
  • BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
    BMC Bioinformatics, Vol. 8 (12 November 2007), 439.
    by Ernest Turro, Natalia Bochkina, Anne-Mette K Hein, Sylvia Richardson
    posted to affymetrix algorithm bayesian bioconductor bioinformatics software statistics by waszak on 2007-11-16 09:35:31 as ***** along with 3 people jyuh jfr shigepong
  • Trends in the quality of data from 5168 oligonucleotide microarrays from a single facility.
    J Biomol Tech, Vol. 16, No. 2. (June 2005), pp. 143-153.
    by DB Finkelstein
    posted to affymetrix microarray qc statistics by waszak on 2007-11-13 20:09:49 as ** along with 1 person ghattem
  • Integrated detection and population-genetic analysis of SNPs and copy number variation.
    Nature genetics (7 September 2008)
    by Steven A A McCarroll, Finny G G Kuruvilla, Joshua M M Korn, Simon Cawley, James Nemesh, Alec Wysoker, Michael H H Shapero, Paul I W I de Bakker, Julian B B Maller, Andrew Kirby, Amanda L L Elliott, Melissa Parkin, Earl Hubbell, Teresa Webster, Rui Mei, James Veitch, Patrick J J Collins, Robert Handsaker, Steve Lincoln, Marcia Nizzari, John Blume, Keith W W Jones, Rich Rava, Mark J J Daly, Stacey B B Gabriel, David Altshuler
    posted to snp hapmap genetics cnv affymetrix by waszak on 2008-10-08 15:11:10 as ** along with 11 people and 1 group caseybrown rsantana Zephyrus psique jbsaltz Ema misonneh djkt daed rdiaz jyuh Roswell Cancer Crosstalk
  • Regulation of rtt107 recruitment to stalled DNA replication forks by the cullin rtt101 and the rtt109 acetyltransferase.
    Molecular biology of the cell, Vol. 19, No. 1. (January 2008), pp. 171-180.
    by TM Roberts, IW Zaidi, JA Vaisica, M Peter, GW Brown
    posted to yeast tiling microarray affymetrix by waszak on 2008-10-08 17:43:34 as **
  • Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer.
    Lancet, Vol. 365, No. 9460. (5 2005), pp. 671-679.
    by Y Wang, JG Klijn, Y Zhang, AM Sieuwerts, MP Look, F Yang, D Talantov, M Timmermans, ME Meijer-van Gelder, J Yu, T Jatkoe, EM Berns, D Atkins, JA Foekens
    posted to affymetrix breast cancer microarray by tuck on 2006-04-18 21:45:40 as ** along with 7 people and 2 groups laral jfr giovanni frohike cberry giovenko winterschlaefer Bioinformatics GeschwindLab
  • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.
    Nucleic Acids Res, Vol. 33, No. 20. (2005)
    by M Dai, P Wang, AD Boyd, G Kostov, B Athey, EG Jones, WE Bunney, RM Myers, TP Speed, H Akil, SJ Watson, F Meng
    posted to affymetrix genome by tuck on 2006-01-26 18:26:50 as ** along with 2 people pcahan1 jfr
  • A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
    Journal of the American Statistical Association, Vol. 99, No. 468., 909.
    by Zhijin Wu, Rafael A Irizarry, Robert Gentleman, Francisco Martinez-Murillo, Forrest Spencer
    posted to affymetrix gcrma microarray normalization by thomlo on 2007-07-03 07:27:28 as ** along with 5 people GeeSharpMinor RMGraze nicholso jo_davies bertelsen
  • AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
    Bioinformatics, Vol. 23, No. 18. (27 July 2007), pp. 2385-2390.
    by Hongfang Liu, Barry RR Zeeberg, Qu Gang, Gunes, Alessandro Ferrucci, Ari Kahn, Michael CC Ryan, Antej Nuhanovic, Peter JJ Munson, William CC Reinhold, David WW Kane, John NN Weinstein
    posted to affymetrix bio-tools correction methods by ryanraaum on 2007-09-17 14:18:46 as ** along with 7 people giovenko jyuh jfr ghattem heliopais Montrachet bertelsen
  • Evaluation in mammalian oocytes of gene transcripts linked to epigenetic reprogramming.
    Reproduction, Vol. 134, No. 4. (October 2007), pp. 549-558.
    by RS Oliveri, M Kalisz, CK Schjerling, CY Andersen, R Borup, AG Byskov
    posted to affymetrix development epigenetics expression gene microarray oocyte oogenesis transcription by rschulz on 2007-12-12 13:21:31 as read
  • Postmeiotic sex chromatin in the male germline of mice.
    Curr Biol, Vol. 16, No. 7. (4 April 2006), pp. 660-667.
    by SH Namekawa, PJ Park, LF Zhang, JE Shima, JR McCarrey, MD Griswold, JT Lee
    posted to affymetrix cell epigenetics expression gene germ germline male microarray sperm transcription x-inactivation by rschulz on 2007-12-12 13:34:44 as read along with 1 person altotor
  • Transcript profiling during mouse oocyte development and the effect of gonadotropin priming and development in vitro.
    Dev Biol, Vol. 286, No. 2. (15 October 2005), pp. 493-506.
    by H Pan, MJ O'brien, K Wigglesworth, JJ Eppig, RM Schultz
    posted to affymetrix development expression gene microarray oocyte oogenesis transcription by rschulz on 2007-12-12 13:13:51 as read
  • Stochastic models inspired by hybridization theory for short oligonucleotide arrays.
    J Comput Biol, Vol. 12, No. 6. (g 2005), pp. 882-893.
    by Z Wu, RA Irizarry
    posted to affymetrix algorithm expression gcrma gene microarray summary by rschulz on 2007-12-12 10:33:03 as read along with 2 people miguel nicholso
  • RefPlus : an R package extending the RMA Algorithm.
    Bioinformatics (10 July 2007)
    by Chris Harbron, Kai-Ming M Chang, Marie C C South
    posted to affymetrix microarray r by rdiaz on 2007-09-27 13:36:40 as ** along with 3 people heliopais jyuh ghattem
  • Detecting genetic variation in microarray expression data
    Genome Res. (3 July 2007), gr.6307307.
    by Jennifer A Greenhall, Matthew A Zapala, Mario Caceres, Ondrej Libiger, Carrolee Barlow, Nicholas J Schork, David J Lockhart
    posted to affymetrix arrays genetic snp variation by rdiaz on 2007-07-19 17:16:22 as ** along with 6 people and 2 groups jyuh jfr eckart_bindewald giovanni qmwwallace msomel Bioinformatics GeschwindLab
  • Spotting variation from expression profiles
    Nature Reviews Genetics, Vol. 8, No. 8., pp. 570-571.
    by Louisa Flintoft
    posted to affymetrix genetic snp variation by rdiaz on 2007-07-19 17:15:37 as **
  • A method for cross-species gene expression analysis with high-density oligonucleotide arrays.
    Nucleic acids research, Vol. 32, No. 11. (2004)
    by W Ji, W Zhou, K Gregg, N Yu, S Davis, S Davis
    posted to affymetrix cross-species sara by ptrobajo on 2008-05-07 16:20:47 as **
  • Quantitative noise analysis for gene expression microarray experiments
    Proceedings of the National Academy of Sciences, Vol. 99, No. 22. (29 October 2002), pp. 14031-14036.
    by Y Tu, G Stolovitzky, U Klein
    posted to affymetrix analysis herman microarray noise by ptrobajo on 2008-05-13 22:00:44 as **
  • Analysis of probe level patterns in Affymetrix microarray data
    BMC Bioinformatics, Vol. 8 (04 May 2007), 146.
    by Alexander C Cambon, Abdelnaby Khalyfa, Nigel GF Cooper, Caryn M Thompson
    posted to affymetrix analysis emiel microarray probe by ptrobajo on 2008-08-06 10:49:11 as ** along with 4 people jfr ghattem niallhaslam bertelsen
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