Tag low_level [65 articles] Export

Recent papers classified by the tag low_level.

	Adaptable gene-specific dye bias correction for two-channel DNA microarrays. [My Copy] Molecular systems biology, Vol. 5 (28 April 2009) by Thanasis Margaritis, Philip Lijnzaad, Dik van Leenen, et al.Diane Bouwmeester, Patrick Kemmeren, Sander R. van Hooff, Frank C. Holstege posted to two-color microarray_analysis low_level dye_bias bioconductor by jfr on 2009-11-09 11:39:03 as along with 1 person reyez
	Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips [My Copy] Brief Bioinform, Vol. 10, No. 3. (1 May 2009), pp. 259-277. by William B. Langdon, Graham J. G. Upton, Andrew P. Harrison posted to low_level affy by jfr on 2009-11-04 11:09:53 as along with 2 people bertelsen zufar
	Statistical methods of background correction for Illumina BeadArray data [My Copy] Bioinformatics, Vol. 25, No. 6. (15 March 2009), pp. 751-757. by Yang Xie, Xinlei Wang, Michael Story posted to low_level illumina beads by jfr on 2009-11-02 14:55:57 as along with 7 people and 1 group ptrobajo welliegirl rdiaz Stew heliopais dswan guhjy Bioinformatics - CRUK
	Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology. [My Copy] Nucleic acids research, Vol. 36, No. 10. (1 June 2008), e58. by Liang-Hao H. Ding, Yang Xie, Seongmi Park, Guanghua Xiao, Michael D. Story posted to illumina low_level by jfr on 2009-07-22 12:47:22 as along with 4 people shikin ptrobajo inesdesantiago guhjy
	Inverse Langmuir method for oligonucleotide microarray analysis. [My Copy] BMC bioinformatics, Vol. 10 (20 February 2009), 64. by G. C. Mulders, G. T. Barkema, E. Carlon posted to affy low_level by jfr to the group Bioinformatics on 2009-07-09 13:03:12 as
	Quality assessment and data analysis for microRNA expression arrays. [My Copy] Nucleic acids research, Vol. 37, No. 2. (1 February 2009), e17. by D. Sarkar, R. Parkin, S. Wyman, et al.A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, M. Tewari posted to low_level microarray_technology mirna quality_control by jfr to the group microRNA on 2009-06-16 17:19:46 as along with 6 people and 1 group Stew nuin ptrobajo baldigroup guhjy giovenko Bioinformatics - CRUK
	Microarray background correction: maximum likelihood estimation for the normal-exponential convolution [My Copy] Biostat (8 December 2008), kxn042. by Jeremy D. Silver, Matthew E. Ritchie, Gordon K. Smyth posted to low_level microarray_analysis two-color by jfr on 2009-06-16 16:24:31 as along with 4 people rdiaz guhjy flips renatomilani
	arrayQualityMetrics--a bioconductor package for quality assessment of microarray data [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 415-416. by Audrey Kauffmann, Robert Gentleman, Wolfgang Huber posted to bioconductor low_level quality_control r by jfr on 2009-04-20 10:30:00 as along with 16 people and 1 group jperkins VGreiff Zephyrus daforerog shikin lwaldron ptrobajo rdiaz siebert bertelsen pkonings dswan renatomilani rschulz nuin guhjy Bioinformatics
	CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Paolo Uva, Emanuele de Rinaldis posted to low_level quality_control r software by jfr on 2009-04-20 10:10:53 as along with 4 people guhjy natstreet druvus GeeSharpMinor
	Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms. [My Copy] Statistical methods in medical research (19 January 2009) by Andy G G. Lynch, M J J. Dunning, M Iddawela, N L L. Barbosa-Morais, M E E. Ritchie posted to illumina low_level by jfr on 2009-04-14 11:36:23 as along with 1 person daforerog
	Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures. [My Copy] Journal of microbiological methods, Vol. 76, No. 2. (February 2009), pp. 188-195. by R. A. Rule, A. E. Pozhitkov, P. A. Noble posted to affy low_level by jfr on 2009-03-12 11:20:12 as
	Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays [My Copy] Bioinformatics, Vol. 25, No. 1. (1 January 2009), pp. 36-41. by Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo posted to affy low_level by jfr on 2009-03-11 11:05:44 as along with 2 people renatomilani guhjy
	Cross-Hybridization Modeling on Affymetrix Exon Arrays. [My Copy] Bioinformatics (Oxford, England) (4 November 2008) by Karen Kapur, Hui Jiang, Yi Xing, Wing Hung H. Wong posted to exon_arrays low_level by jfr on 2009-03-11 11:04:54 as along with 3 people dswan GeeSharpMinor rschulz
	A competitive hybridization model predicts probe signal intensity on high density DNA microarrays [My Copy] Nucl. Acids Res., Vol. 36, No. 20. (1 November 2008), pp. 6585-6591. by Shuzhao Li, Alex Pozhitkov, Marius Brouwer posted to low_level microarray_technology by jfr on 2009-02-25 14:53:58 as along with 3 people bertelsen rdiaz ojabado
	Mapping short DNA sequencing reads and calling variants using mapping quality scores. [My Copy] Genome research, Vol. 18, No. 11. (19 November 2008), pp. 1851-1858. by Heng Li, Jue Ruan, Richard Durbin posted to deep_sequencing low_level quality_control by jfr on 2009-02-23 11:34:50 as along with 35 people and 2 groups cthachuk darshan adijr darian bozdagd jmanning2k stubrown APRegier ghattem jbhiatt mmartin michaelbarton polivares jonilaserson humburg n00c jessopher maren GeeSharpMinor vmsr vplagnol natstreet poschm druvus dandaman xingxu rschulz jmcq inesdesantiago Neeperando nmohelli matthewsuderman bpb gdb farhat SIMR bioinformatics BergmanLab
	Probabilistic base calling of Solexa sequencing data. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 431. by Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef posted to deep_sequencing low_level quality_control by jfr on 2009-02-20 16:36:20 as along with 16 people and 1 group heliopais orzenil n00c dakelley usagi-kirin magusina malcook natstreet druvus iris42 abizar caseybrown reyez pengchy waszak nuin SIMR bioinformatics
	Statistical challenges in preprocessing in microarray experiments in cancer. [My Copy] Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 14, No. 19. (1 October 2008), pp. 5959-5966. by K. Owzar, W. T. Barry, S. H. Jung, I. Sohn, S. L. George posted to low_level microarray_analysis review by jfr on 2009-01-29 11:05:43 as along with 7 people and 1 group zufar lwaldron Zephyrus rdiaz shikin guhjy winterschlaefer Bioinformatics
	Effect of single nucleotide polymorphisms on Affymetrix(R) match-mismatch probe pairs. [My Copy] Bioinformation, Vol. 2, No. 9. (2008), pp. 405-411. by E. C. Rouchka, A. W. Phatak, A. V. Singh posted to affy low_level snp by jfr on 2009-01-09 11:31:45 as
	"Hook"-calibration of GeneChip-microarrays: Theory and algorithm [My Copy] Algorithms for Molecular Biology, Vol. 3, No. 1. (2008) by Hans Binder, Stephan Preibisch posted to affy low_level quality_control by jfr on 2008-11-06 11:40:47 as along with 3 people zufar bertelsen talponer
	"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures [My Copy] Algorithms for Molecular Biology, Vol. 3, No. 1. (2008) by Hans Binder, Knut Krohn, Stephan Preibisch posted to affy low_level quality_control by jfr on 2008-11-06 11:40:02 as along with 2 people bertelsen talponer
	Spike-in validation of an Illumina-specific variance-stabilizing transformation. [My Copy] BMC research notes, Vol. 1 (2008) by M. J. Dunning, M. E. Ritchie, N. L. Barbosa-Morais, S. Tavaré, A. G. Lynch posted to illumina low_level normalization by jfr on 2008-10-23 14:02:03 as along with 1 person Stew
	I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2897-2902. by Willem Talloen, Djork-Arne Clevert, Sepp Hochreiter, et al.Dhammika Amaratunga, Luc Bijnens, Stefan Kass, Hinrich W. Gohlmann posted to affy low_level by jfr on 2008-09-19 15:34:15 as along with 2 people cassj aviad_work
	Methods for evaluating gene expression from Affymetrix microarray datasets. [My Copy] BMC bioinformatics, Vol. 9 (17 June 2008), 284. by Ning Jiang, Lindsey J. Leach, Xiaohua Hu, et al.Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei W. Luo posted to affy low_level by jfr on 2008-09-16 18:57:54 as along with 7 people daforerog GeeSharpMinor heliopais caseybrown tonia_schwartz guhjy winterschlaefer
	A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (14 April 2008), 194. by Huanying Ge, Chao Cheng, Lei Li posted to affy low_level normalization by jfr on 2008-06-17 17:25:42 as along with 1 person VGreiff
	Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed. [My Copy] Physical biology, Vol. 5, No. 1. (2008) by C. J. Burden posted to affy low_level by jfr on 2008-05-16 10:27:30 as
	Normalization of oligonucleotide arrays based on the least-variant set of genes [My Copy] BMC Bioinformatics, Vol. 9 (05 March 2008), 140. by Stefano Calza, Davide Valentini, Yudi Pawitan posted to affy gene_expression low_level normalization software by jfr on 2008-05-05 10:58:52 as along with 5 people bertelsen waszak guhjy giovenko GeeSharpMinor
	Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction [My Copy] Nucl. Acids Res., Vol. 36, No. 7. (1 April 2008), pp. 2395-2405. by Hinanit Koltai, Carmiya Weingarten-Baror posted to low_level microarray_technology by jfr on 2008-04-30 15:44:25 as along with 3 people bertelsen guhjy ptrobajo
	AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip(TM) expression arrays with respect to SNPs [My Copy] BMC Bioinformatics, Vol. 8 (30 July 2007), 276. by Sunita Kumari, Lalit K. Verma, Jennifer W. Weller posted to affy low_level methodology software by jfr on 2008-02-13 13:45:39 as along with 1 person guhjy
	A comparison of background correction methods for two-colour microarrays [My Copy] Bioinformatics, Vol. 23, No. 20. (15 October 2007), pp. 2700-2707. by Matthew E. Ritchie, Jeremy Silver, Alicia Oshlack, et al.Melissa Holmes, Dileepa Diyagama, Andrew Holloway, Gordon K. Smyth posted to low_level normalization two-color by jfr on 2008-02-05 11:39:32 as along with 7 people bertelsen guhjy shigepong GeeSharpMinor debasis caseybrown Stew
	Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2566-2572. by Chunlei Wu, Haitao Zhao, Keith Baggerly, Roberto Carta, Li Zhang posted to affy low_level by jfr on 2008-02-04 11:50:29 as along with 1 person niallhaslam
	CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1700-1701. by H. Zhao, K. Engelen, B. De Moor, K. Marchal posted to bioconductor low_level software two-color by jfr on 2008-01-24 17:19:04 as along with 2 people guhjy GeeSharpMinor
	Analysis of probe level patterns in Affymetrix microarray data [My Copy] BMC Bioinformatics, Vol. 8 (04 May 2007), 146. by Alexander C. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson posted to affy annotation low_level by jfr on 2008-01-24 17:16:35 as along with 4 people ghattem niallhaslam bertelsen ptrobajo
	Stratification bias in low signal microarray studies [My Copy] BMC Bioinformatics, Vol. 8 (02 September 2007), 326. by Brian J. Parker, Simon Gunter, Justin Bedo posted to low_level by jfr on 2007-12-06 10:44:57 as along with 2 people shigepong guhjy
	arrayQCplot: software for checking the quality of microarray data. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 18. (15 September 2006), pp. 2305-2307. by Eun-Kyung K. Lee, Sung-Gon G. Yi, Taesung Park posted to low_level quality_control software by jfr on 2007-12-05 10:35:09 as along with 2 people shikin daforerog
	Estimation and correction of non-specific binding in a large-scale spike-in experiment [My Copy] Genome Biology, Vol. 8 (26 June 2007), R126. by Eugene F. Schuster, Eric Blanc, Linda Partridge, Janet Thornton posted to affy low_level by jfr on 2007-12-05 10:24:09 as along with 1 person bertelsen
	Correcting for sequence biases in present/absent calls [My Copy] Genome Biology, Vol. 8 (26 June 2007), R125. by Eugene F. Schuster, Eric Blanc, Linda Partridge, Janet Thornton posted to affy low_level by jfr on 2007-12-05 10:21:45 as
	The utility of MAS5 expression summary and detection call algorithms [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Stuart Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller posted to affy low_level normalization by jfr on 2007-12-04 15:22:25 as along with 7 people dswan lwaldron frohike heliopais ryanraaum wirawan waszak
	Autocorrelation analysis reveals widespread spatial biases in microarray experiments [My Copy] BMC Genomics, Vol. 8, No. 1. (12 June 2007), 164. by Amnon Koren, Itay Tirosh, Naama Barkai posted to low_level by jfr on 2007-12-03 10:56:59 as along with 1 person giovenko
	Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips [My Copy] BMC Bioinformatics, Vol. 8 (11 June 2007), 195. by Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo posted to affy low_level by jfr on 2007-11-28 13:21:17 as along with 1 person heliopais
	Pre-processing Agilent microarray data [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, et al.Robert Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope posted to agilent low_level by jfr on 2007-11-26 18:13:20 as along with 7 people lwaldron coela ajeffs nuin jhatrimatri shigepong bertelsen
	The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by R. G. Verhaak, F. J. Staal, P. J. Valk, B. Lowenberg, M. J. Reinders, D. de Ridder posted to affy evaluation low_level by jfr on 2007-11-23 15:31:50 as along with 3 people RMGraze ghattem frohike
	chip artifact CORRECTion (caCORRECT): a bioinformatics system for quality assurance of genomics and proteomics array data. [My Copy] Ann Biomed Eng, Vol. 35, No. 6. (June 2007), pp. 1068-1080. by T. H. Stokes, R. A. Moffitt, J. H. Phan, M. D. Wang posted to affy low_level quality_control by jfr on 2007-09-13 14:46:42 as
	Microarray Blob-Defect Removal Improves Array Analysis. [My Copy] Bioinformatics (1 March 2007) by Jun S S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X Shirley Liu posted to affy low_level microarray_technology by jfr on 2007-07-31 17:12:32 as along with 5 people and 1 group kengg shigepong ghattem caseybrown waszak Plantandetc
	How high is the level of technical noise in microarray data? [My Copy] Biology Direct, Vol. 2 (11 April 2007), 9. by Lev Klebanov, Andrei Yakovlev posted to affy low_level by jfr on 2007-07-10 11:36:56 as along with 2 people ghattem heliopais
	Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data [My Copy] BMC Bioinformatics, Vol. 8 (25 January 2007), 26. by Andy G. Lynch, David E. Neal, John D. Kelly, Glyn J. Burtt, Natalie P. Thorne posted to low_level microarray_technology two-color by jfr on 2007-05-14 14:13:00 as along with 1 person shigepong
	PQN and DQN: algorithms for expression microarrays. [My Copy] J Theor Biol, Vol. 243, No. 2. (21 November 2006), pp. 273-278. by W. M. Liu, R. Li, J. Z. Sun, et al.J. Wang, J. Tsai, W. Wen, A. Kohlmann, P. M. Williams posted to affy low_level methodology by jfr on 2007-05-11 14:43:09 as
	Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. [My Copy] Biostatistics (Oxford, England), Vol. 8, No. 2. (22 April 2007), pp. 485-499. by Benilton Carvalho, Henrik Bengtsson, Terence P. Speed, Rafael A. Irizarry posted to genotyping low_level methodology snp-arrays by jfr on 2007-01-16 18:06:34 as along with 4 people shikin daforerog GeeSharpMinor guhjy
	When should one subtract background fluorescence in two color microarrays? [My Copy] Biostatistics (12 December 2006) by Robert B B. Scharpf, Christine A A. Iacobuzio-Donahue, Julie B B. Sneddon, Giovanni Parmigiani posted to two-color low_level by jfr on 2007-01-12 16:48:00 as along with 3 people rdiaz shigepong ugengma
	Robust estimators for expression analysis [My Copy] Bioinformatics, Vol. 18, No. 12. (1 December 2002), pp. 1585-1592. by Earl Hubbell, Wei-Min Liu, Rui Mei posted to methodology low_level affy by jfr on 2007-01-11 13:55:03 as along with 7 people and 1 group humburg bertelsen lawraga VGreiff vertikalist GeeSharpMinor wirawan BTS-PT-AS-CS
	Feature-level exploration of a published Affymetrix GeneChip control dataset [My Copy] Genome Biology, Vol. 7 (01 September 2006), 404. by Rafael A. Irizarry, Leslie M. Cope, Zhijin Wu posted to normalization low_level affy by jfr on 2007-01-10 15:46:49 as along with 2 people bertelsen ghattem

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affy	37
normalization	10
quality_control	10
microarray_technology	9
two-color	9
software	6
illumina	4
methodology	4
bioconductor	3
evaluation	3
microarray_analysis	3
bioinformatics	2
co-expression	2
deep_sequencing	2
mirna	2
r	2
agilent	1
annotation	1
beads	1
dye_bias	1
exon_arrays	1
gene_expression	1
genotyping	1
image_analysis	1
mass_spec	1
review	1
snp	1
snp-arrays	1

Tag low_level [65 articles] Export

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