Tag affymetrix [at least 200 articles] Export

Recent papers classified by the tag affymetrix.

	Exon Array Analyzer: a web interface for Affymetrix exon array analysis [My Copy] Bioinformatics (12 October 2009), btp577. by Pascal Gellert, Shizuka Uchida, Thomas Braun posted to webserver microarray exon analysis affymetrix by neils on 2009-10-25 01:33:18 as
	Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. [My Copy] Genome biology, Vol. 9, No. 4. (3 April 2008), R63. by Shin Lin, Benilton Carvalho, David J. Cutler, Dan E. Arking, Aravinda Chakravarti, Rafael A. Irizarry posted to snp calling bayesian affymetrix by rdiaz on 2009-10-23 14:19:08 as along with 5 people shikin daforerog maren natstreet jfr
	A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip(R) whole-genome resequencing platform [My Copy] Nucl. Acids Res. (15 November 2007), gkm918. by Gagan A. Pandya, Michael H. Holmes, Sirisha Sunkara, et al.Andrew Sparks, Yun Bai, Kathleen Verratti, Kelly Saeed, Pratap Venepally, Behnam Jarrahi, Robert D. Fleischmann, Scott N. Peterson posted to snp francisella affymetrix by druvus on 2009-09-30 12:22:50 as along with 2 people giovanni niallhaslam
	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 summary probeset microarray expression estimates affymetrix by bertelsen on 2009-09-28 14:40:28 as along with 7 people and 1 group humburg lawraga VGreiff vertikalist GeeSharpMinor jfr wirawan BTS-PT-AS-CS
	Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. [My Copy] BMC proceedings, Vol. 3 Suppl 4 (2009) by Pieter Bt B. Neerincx, Pierrot Casel, Dennis Prickett, et al.Haisheng Nie, Michael Watson, Jack Am A. Leunissen, Martien Am A. Groenen, Christophe Klopp posted to probe-level pipelines microarray comparison annotation affymetrix by bertelsen on 2009-09-27 18:24:49 as
	Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis. [My Copy] In silico biology, Vol. 7, No. 3. (2007), pp. 241-260. by Yuriy L. Orlov, Jiangtao Zhou, Leonard Lipovich, Atif Shahab, Vladimir A. Kuznetsov posted to sequence quality-control quality-assessment probe-level microarray mapping expression data analysis affymetrix by bertelsen on 2009-09-27 18:22:25 as along with 1 person cottrell
	Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples [My Copy] PLoS ONE, Vol. 4, No. 5. (21 May 2009), e5645. by Balazs Gyorffy, Bela Molnar, Hermann Lage, Zoltan Szallasi, Aron C. Eklund posted to review preprocessing comparison algorithm affymetrix by rdiaz on 2009-09-23 17:27:51 as along with 1 person bertelsen
	A first principles approach to differential expression in microarray data analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 292. by Robert Rubin posted to expression differential anova affymetrix by rdiaz on 2009-09-17 14:09:02 as along with 5 people dswan brianb neils renatomilani torfinnnome
	A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. [My Copy] BMC bioinformatics, Vol. 8 (20 April 2007), 132. by Rudi Alberts, Peter Terpstra, Menno Hardonk, et al.Leonid V. Bystrykh, Gerald de Haan, Rainer Breitling, Jan-Peter P. Nap, Ritsert C. Jansen posted to reannotation rat mouse human affymetrix by ptrobajo on 2009-09-17 10:52:09 as along with 4 people heliopais guhjy jfr ghattem
	Integrating probe-level expression changes across generations of Affymetrix arrays. [My Copy] Nucleic acids research, Vol. 33, No. 22. (2005), pp. e193-e193. by Laura L. Elo, Leo Lahti, Heli Skottman, Minna Kyläniemi, Riitta Lahesmaa, Tero Aittokallio posted to reannotation probe-level integration compendium affymetrix by ptrobajo on 2009-09-17 09:47:53 as along with 1 person heliopais
	Submicroscopic genomic alterations in Silver-Russell syndrome and Silver-Russell-like patients. [My Copy] Journal of medical genetics (14 September 2009) by Sara Bruce, Katariina Hannula-Jouppi, Mari Puoskari, et al.Ingegerd Fransson, Kalle Oj O. Simola, Marita Lipsanen-Nyman, Juha Kere posted to srs microarray human epigenetics disease cgh affymetrix by rschulz on 2009-09-16 12:44:58 as along with 1 person Terkko
	Celsius: a community resource for Affymetrix microarray data. [My Copy] Genome biology, Vol. 8, No. 6. (14 June 2007), R112. by Allen Day, Marc R. Carlson, Jun Dong, Brian D. O'Connor, Stanley F. Nelson posted to r-package microarray compendium affymetrix by ptrobajo on 2009-09-12 22:38:36 as along with 5 people jeremymiller jfr gpalidwor ghattem orzenil
	Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. [My Copy] Plant methods, Vol. 1, No. 1. (2005) by John P. Hammond, Martin R. Broadley, David J. Craigon, et al.Janet Higgins, Zoe F. Emmerson, Henrik J. Townsend, Philip J. White, Sean T. May posted to probe-selection probe oligonucleotide microarray heterologous genechip dna affymetrix by bertelsen on 2009-09-03 15:21:44 as along with 1 person natstreet
	Affy exon tissues: exon levels in normal tissues in human, mouse and rat [My Copy] Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2442-2443. by Andrew A. Pohl, Charles W. Sugnet, Tyson A. Clark, Kayla Smith, Pauline A. Fujita, Melissa S. Cline posted to tissues rat normal mouse levels human exon comparative array affymetrix by dswan on 2009-09-01 09:41:17 as along with 1 person guhjy
	Single-feature polymorphism discovery by computing probe affinity shape powers [My Copy] BMC Genetics, Vol. 10, No. 1. (2009), 48. by Wayne W. Xu, Seungho Cho, Samuel S. Yang, et al.Yung T. Bolon, Hatice Bilgic, Haiyan Jia, Yanwen Xiong, Gary Muehlbauer posted to snp affymetrix by pkonings on 2009-08-27 09:38:35 as
	A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 17. (1 September 2009), pp. 2149-2156. by Henrik Bengtsson, Pratyaksha Wirapati, Terence P. Speed posted to preprocessing cnv affymetrix by pkonings on 2009-08-20 09:24:38 as along with 5 people shikin djkt rdiaz daforerog neils
	Non-linear analysis of GeneChip arrays [My Copy] Nucl. Acids Res., Vol. 34, No. 15. (26 August 2006), pp. gkl435-e105. by Diana Abdueva, Dmitriy Skvortsov, Simon Tavare posted to preprocessing affymetrix by ericrpaquet on 2009-08-18 20:16:46 as
	Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity. [My Copy] Algorithms for molecular biology : AMB, Vol. 4, No. 1. (22 April 2009), 7. by Koji Kadota, Yuji Nakai, Kentaro Shimizu posted to rma preprocessing plier expression differential affymetrix by ericrpaquet on 2009-08-18 20:11:32 as along with 5 people bertelsen daforerog dswan renatomilani lptolik
	Probe set algorithms: is there a rational best bet? [My Copy] BMC bioinformatics, Vol. 7 (30 August 2006), 395. by Jinwook Seo, Eric P. Hoffman posted to rma plier gcrma affymetrix by ericrpaquet on 2009-08-18 20:00:27 as along with 7 people lwaldron heliopais jfr ghattem rschulz bertelsen shikin
	Genome-wide analysis of antisense transcription with Affymetrix exon array [My Copy] BMC Genomics, Vol. 9, No. 1. (22 January 2008), 27. by Xijin Ge, Wendy Rubinstein, Yong C. Jung, Qingfa Wu posted to affymetrix analysis antisense array exon genome transcription wide by dswan to the group Bioinformatics on 2009-08-11 11:11:26 as
	AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 18. (15 September 2007), pp. 2385-2390. by Hongfang Liu, Barry R. Zeeberg, Gang Qu, et al.A. Gunes Koru, Alessandro Ferrucci, Ari Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein posted to affymetrix bioinformatics microarrays by VGreiff on 2009-08-04 20:30:42 as along with 8 people giovenko guhjy jfr ghattem ryanraaum heliopais Montrachet bertelsen
	Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation. [My Copy] Nucleic acids research (7 July 2009), gkp559. by Lin Wan, Kelian Sun, Qi Ding, et al.Yuehua Cui, Ming Li, Yalu Wen, Robert C. Elston, Minping Qian, Wenjiang J. Fu posted to affymetrix cnv by pkonings on 2009-08-04 09:53:31 as along with 2 people rdiaz guhjy
	Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies [My Copy] Genome Biology, Vol. 10, No. 7. (2009), R77. by Essi Laajala, Tero Aittokallio, Riitta Lahesmaa, Laura Elo posted to affymetrix differential exon microarray splicing statistics by neils on 2009-07-17 00:39:38 as along with 3 people ericrpaquet lwaldron djkt
	Construction and use of gene expression covariation matrix [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 214. by Jerome Hennetin, Petri Pehkonen, Michel Bellis posted to affymetrix bioinformatics coexpression covariation microarray single-channel by rschulz on 2009-07-15 14:17:44 as along with 2 people dipenps jmeppley
	A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 2. (22 January 2003), pp. 185-193. by B. M. Bolstad, R. A. Irizarry, M. Astrand, T. P. Speed posted to affymetrix comparison methods microarray normalization statistics by neils on 2009-07-09 00:51:06 as along with 22 people jperkins vplagnol brianb ipark-kaist shikin michaelbarton emptyhb noushin huiminC cassj Dax42 pcahan1 chad_davis RMGraze gjuggler filmsternchen qmwwallace joepickrell ghattem bertelsen vertikalist GeeSharpMinor
	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 affymetrix background bioinformatics biophysics cross-hybridization genechip probe probe-level by bertelsen on 2009-06-28 09:54:31 as along with 2 people jfr zufar
	"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 affymetrix algorithm calibration gene-expression genechip microarray quantitative theory by bertelsen on 2009-06-27 10:08:47 as along with 3 people zufar talponer jfr
	A new summarization method for affymetrix probe level data [My Copy] Bioinformatics, Vol. 22, No. 8. (15 April 2006), pp. 943-949. by Sepp Hochreiter, Djork-Arne Clevert, Klaus Obermayer posted to affymetrix bayesian factor-analysis genechip method microarray probe-level probe-summarization by bertelsen on 2009-06-27 09:10:10 as along with 3 people shikin cassj ghattem
	Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression [My Copy] BMC Bioinformatics, Vol. 7 (25 August 2006), 391. by Sebastien Lemieux posted to accuracy affymetrix detection differential gene-expression genechip microarray mixture modeling probe-level by bertelsen on 2009-06-26 22:15:30 as
	Towards the uniform distribution of null P values on Affymetrix microarrays [My Copy] Genome Biology, Vol. 8, No. 5. (01 May 2007), R69. by Anthony A. Fodor, Timothy L. Tickle, Christine Richardson posted to affymetrix false-discovery microarray normalization null-distribution p-value t-test variance by bertelsen on 2009-06-24 13:56:48 as along with 2 people b jfr
	CellMiner: a relational database and query tool for the NCI-60 cancer cell lines [My Copy] BMC Genomics, Vol. 10, No. 1. (2009), 277. by Uma Shankavaram, Sudhir Varma, David Kane, et al.Margot Sunshine, Krishna Chary, William Reinhold, Yves Pommier, John Weinstein posted to acgh affymetrix analysis cancer cell database integrated lines microarray mirna mrna by fpattyn on 2009-06-24 13:03:10 as
	An overview of image-processing methods for Affymetrix GeneChips. [My Copy] 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 genechip image-processing method overview review by bertelsen on 2009-06-22 22:19:55 as along with 6 people and 1 group lwaldron neils guhjy jfr aswin yevishere Bioinformatics
	Expression Profiling Using Affymetrix GeneChip Microarrays. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 509 (2009), pp. 35-46. by H. Auer, D. L. Newsom, K. Kornacker posted to affymetrix expression genechip medical microarray profiling therapeutic by bertelsen on 2009-06-22 22:15:19 as
	Systematic order dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips(R). [My Copy] Bioinformatics (25 September 2007) by Kathe E E. Bjork, Karen Kafadar posted to affymetrix genechip by bertelsen on 2009-06-22 22:01:55 as along with 2 people cassj ghattem
	Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays [My Copy] BMC Genomics, Vol. 9 (07 November 2008), 529. by Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J. Gaffney, Roderick V. Jensen, Jacek Majewski posted to affymetrix analysis array exon gene-expression genechip isoform splicing variation by bertelsen on 2009-06-22 17:17:29 as along with 6 people jfr guhjy ivanek pengchy dswan caseybrown
	Global correlation analysis between redundant probe sets using a large collection of Arabidopsis ath1 expression profiling data. [My Copy] Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference (2006), pp. 223-226. by X. Cui, A. Loraine posted to affymetrix microarray multiple-probe probe by sebastien_vigneau on 2009-06-17 16:12:42 as
	Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing [My Copy] PLoS ONE, Vol. 4, No. 1. (23 January 2009), e4229. by Xiangqin Cui, Ann E. Loraine posted to affymetrix microarray mrna mrna-processing multiple-probe polyadenylation probe three-prime-expression-array by sebastien_vigneau on 2009-06-17 16:08:26 as along with 1 person ivanek
	Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips [My Copy] BMC Bioinformatics, Vol. 8 (15 January 2007), 13. by Maria A. Stalteri, Andrew P. Harrison posted to affymetrix microarray multiple-probe probe by sebastien_vigneau on 2009-06-17 16:02:47 as along with 8 people guhjy jfr gpalidwor hpiwowar frohike ghattem bertelsen heliopais
	Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach [My Copy] Genomics, Vol. 85, No. 3. (March 2005), pp. 297-308. by Jinghui Zhang, Richard P. Finney, Robert J. Clifford, Leslie K. Derr, Kenneth H. Buetow posted to affymetrix false-positive microarray multiple-probe probe by sebastien_vigneau on 2009-06-17 16:01:32 as along with 1 person qfwills
	Alternative mapping of probes to genes for Affymetrix chips. [My Copy] BMC Bioinformatics, Vol. 5 (14 August 2004) by L. Gautier, M. Møller, L. Friis-Hansen, S. Knudsen posted to affymetrix microarray multiple-probe probe by sebastien_vigneau on 2009-06-17 16:00:24 as along with 3 people ghattem heliopais bertelsen
	A comparison of Affymetrix gene expression arrays [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Mark Robinson, Terence Speed posted to affymetrix microarray by sebastien_vigneau on 2009-06-17 00:10:31 as along with 3 people jfr hpaces waszak
	High density synthetic oligonucleotide arrays. [My Copy] Nat Genet, Vol. 21, No. 1 Suppl. (January 1999), pp. 20-24. by R. J. Lipshutz, S. P. Fodor, T. R. Gingeras, D. J. Lockhart posted to affymetrix array experiment genechip genomics high-throughput microarray oligonucleotide by bertelsen on 2009-06-16 15:21:29 as along with 3 people and 1 group jeremymiller incovoma shikin GeschwindLab
	Sources of variation in Affymetrix microarray experiments. [My Copy] BMC bioinformatics, Vol. 6 (2005) by Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, et al.Lang Chen, Stephen Barnes, Katherine E. Scheirer, Rudolph S. Parrish, David B. Allison, Grier P. Page posted to affymetrix experiment microarray variation by bertelsen on 2009-06-16 12:01:25 as along with 2 people zufar ghattem
	A benchmark for Affymetrix GeneChip expression measures. [My Copy] Bioinformatics, Vol. 20, No. 3. (12 February 2004), pp. 323-331. by L. M. Cope, R. A. Irizarry, H. A. Jaffee, Z. Wu, T. P. Speed posted to affymetrix benchmark expression genechip measure probe-level summary by bertelsen on 2009-06-16 12:00:00 as along with 3 people heliopais Dax42 ghattem
	A reanalysis of a published Affymetrix GeneChip control dataset. [My Copy] Genome Biol, Vol. 7, No. 3. (22 March 2006) by Alan R. Dabney, John D. Storey posted to affymetrix analysis control dataset genechip by bertelsen on 2009-06-16 11:58:59 as along with 3 people jfr lhonigberg ghattem
	An application for assessing quality of RNA hybridized to Affymetrix GeneChips. [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2699-2701. by K. J. Archer, T. Guennel posted to affymetrix assessment degradation genechip quality rna by bertelsen on 2009-06-16 11:58:25 as along with 3 people jfr ghattem waszak
	Differential splicing using whole-transcript microarrays. [My Copy] BMC bioinformatics, Vol. 10 (22 May 2009), 156. by M. D. Robinson, T. P. Speed posted to affymetrix algorithm differential exon gene microarray rma splicing transcript whole by dswan to the group Bioinformatics on 2009-06-09 11:29:40 as along with 5 people guhjy lwaldron chrisamiller humburg neils
	Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. [My Copy] Genome Biol, Vol. 6, No. 2. (2005) by S. E. Choe, M. Boutros, A. M. Michelson, G. M. Church, M. S. Halfon posted to affymetrix analysis control dataset genechip by bertelsen on 2009-06-09 00:15:44 as along with 8 people and 1 group lwaldron heliopais xwbcn jeremymiller ccr ghattem waszak daforerog GeschwindLab
	Comparison of Affymetrix GeneChip expression measures [My Copy] Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 789-794. by Rafael A. Irizarry, Zhijin Wu, Harris A. Jaffee posted to affymetrix comparison expression genechip measure by bertelsen on 2009-06-09 00:08:24 as along with 7 people zufar heliopais winterschlaefer RMGraze hggr ghattem groepl
	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 affymetrix control dataset exploration feature-level genechip by bertelsen on 2009-06-08 23:16:49 as along with 2 people jfr ghattem

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microarray	209
genechip	49
expression	40
analysis	36
probe-level	22
exon	20
probe	19
annotation	17
normalization	17
statistics	17
algorithm	16
gene	16
rma	15
snp	14
bioconductor	13
differential	13
qc	13
splicing	13
bioinformatics	12
cnv	12
preprocessing	12
array	11
cdna	11
software	11
human	10
cancer	9
control	8
summary	8
transcription	8
bayesian	7
comparison	7
quality	7
variation	7
cross-species	6
dataset	6
experimental_design	6
gene-expression	6
genome	6
oligonucleotide	6
r	6
sara	6
transcriptomics	6
affy	5
antisense	5
data	5
gcrma	5
genomics	5
illumina	5
multiple-probe	5
rna	5
alternate	4
benchmark	4
blood	4
cdf	4
cell	4
compendium	4
database	4
epigenetics	4
experiment	4
mapping	4
measure	4
method	4
overview	4
quality-assessment	4
tiling	4
background	3
calibration	3
cgh	3
degradation	3
design	3
drosophila	3
encode	3
hugene	3
methods	3
model	3
probeset	3
reproducibility	3
review	3
sensitivity	3
sequence	3
specificity	3
t-test	3
target	3
bias	2
biophysics	2
development	2
disease	2
em	2
factor-analysis	2
false-discovery	2
image-processing	2
melanogaster	2
ovarian	2
peripheral	2
quality-control	2
theory	2
treatment	2
web	2
wide	2
yeast	2

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