PubMed

Background correction using dinucleotide affinities improves the performance of GCRMA.

Gharaibeh RZ, Fodor AA, Gibas CJ.

BMC Bioinformatics. 2008 Oct 23;9:452.PMID: 18947404 [PubMed - indexed for MEDLINE]Related articlesFree article

Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.

Gharaibeh RZ, Fodor AA, Gibas CJ.

Comput Biol Chem. 2007 Apr;31(2):92-8. Epub 2007 Feb 20.PMID: 17387043 [PubMed - indexed for MEDLINE]Related articlesFree article

Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP.

Bioinformatics. 2004 Nov 1;20(16):2534-44. Epub 2004 Apr 29.PMID: 15117752 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.

Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S.

BMC Bioinformatics. 2005 Feb 10;6:26.PMID: 15705192 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of methods for oligonucleotide array data via quantitative real-time PCR.

Qin LX, Beyer RP, Hudson FN, Linford NJ, Morris DE, Kerr KF.

BMC Bioinformatics. 2006 Jan 17;7:23.PMID: 16417622 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model.

Sásik R, Calvo E, Corbeil J.

Bioinformatics. 2002 Dec;18(12):1633-40.PMID: 12490448 [PubMed - indexed for MEDLINE]Related articlesFree article

A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data.

Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann RH.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S19.PMID: 19594878 [PubMed - indexed for MEDLINE]Related articlesFree article

A non-transformation method for identifying differentially expressed genes from cDNA microarrays.

Zhang JG, Yin ZJ, Zhang Q.

Yi Chuan Xue Bao. 2006 Jan;33(1):80-8.PMID: 16450591 [PubMed - indexed for MEDLINE]Related articles

A model of molecular interactions on short oligonucleotide microarrays.

Zhang L, Miles MF, Aldape KD.

Nat Biotechnol. 2003 Jul;21(7):818-21. Epub 2003 Jun 8.PMID: 12794640 [PubMed - indexed for MEDLINE]Related articles

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis.

Zhou Y, Abagyan R.

BMC Bioinformatics. 2002;3:3. Epub 2002 Jan 22.PMID: 11835687 [PubMed - indexed for MEDLINE]Related articlesFree article

A power law global error model for the identification of differentially expressed genes in microarray data.

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2004 Dec 17;5:203.PMID: 15606915 [PubMed - indexed for MEDLINE]Related articlesFree article

Normal uniform mixture differential gene expression detection for cDNA microarrays.

Dean N, Raftery AE.

BMC Bioinformatics. 2005 Jul 12;6:173.PMID: 16011807 [PubMed - indexed for MEDLINE]Related articlesFree article

Probe set algorithms: is there a rational best bet?

Seo J, Hoffman EP.

BMC Bioinformatics. 2006 Aug 30;7:395.PMID: 16942624 [PubMed - indexed for MEDLINE]Related articlesFree article

A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.

Charbonnier Y, Gettler B, François P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J.

BMC Genomics. 2005 Jun 17;6:95.PMID: 15963225 [PubMed - indexed for MEDLINE]Related articlesFree article

Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.

Binder H, Preibisch S, Kirsten T.

Langmuir. 2005 Sep 27;21(20):9287-302.PMID: 16171364 [PubMed - indexed for MEDLINE]Related articles

Estimation and correction of non-specific binding in a large-scale spike-in experiment.

Schuster EF, Blanc E, Partridge L, Thornton JM.

Genome Biol. 2007;8(6):R126.PMID: 17594493 [PubMed - indexed for MEDLINE]Related articlesFree article

Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.

Hu Z, Willsky GR.

BMC Bioinformatics. 2006 Jan 10;7:12.PMID: 16403228 [PubMed - indexed for MEDLINE]Related articlesFree article

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

Liu H, Tarima S, Borders AS, Getchell TV, Getchell ML, Stromberg AJ.

BMC Bioinformatics. 2005 Apr 25;6:106.PMID: 15850479 [PubMed - indexed for MEDLINE]Related articlesFree article

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.

Casneuf T, Van de Peer Y, Huber W.

BMC Bioinformatics. 2007 Nov 26;8:461.PMID: 18039370 [PubMed - indexed for MEDLINE]Related articlesFree article

Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling.

Bhattacharya S, Mariani TJ.

Nucleic Acids Res. 2005 Oct 13;33(18):e157.PMID: 16224098 [PubMed - indexed for MEDLINE]Related articlesFree article