PubMed

Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?

Klebanov L, Chen L, Yakovlev A.

Biol Direct. 2007 Nov 7;2:28.PMID: 17988401 [PubMed - indexed for MEDLINE]Related articlesFree article

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.

Okoniewski MJ, Miller CJ.

BMC Bioinformatics. 2006 Jun 2;7:276.PMID: 16749918 [PubMed - indexed for MEDLINE]Related articlesFree article

Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays.

Nieto-Díaz M, Pita-Thomas W, Nieto-Sampedro M.

BMC Genomics. 2007 Apr 3;8:89.PMID: 17407579 [PubMed - indexed for MEDLINE]Related articlesFree article

Stochastic models inspired by hybridization theory for short oligonucleotide arrays.

Wu Z, Irizarry RA.

J Comput Biol. 2005 Jul-Aug;12(6):882-93.PMID: 16108723 [PubMed - indexed for MEDLINE]Related articles

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues.

Popova T, Mennerich D, Weith A, Quast K.

BMC Genomics. 2008 Feb 25;9:91.PMID: 18298816 [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

Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization.

Binder H, Brücker J, Burden CJ.

J Phys Chem B. 2009 Mar 5;113(9):2874-95.PMID: 19708217 [PubMed - indexed for MEDLINE]Related articles

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.

Huang JC, Morris QD, Hughes TR, Frey BJ.

Bioinformatics. 2005 Jun;21 Suppl 1:i222-31.PMID: 15961461 [PubMed - indexed for MEDLINE]Related articlesFree article

Relationship between gene expression and observed intensities in DNA microarrays--a modeling study.

Held GA, Grinstein G, Tu Y.

Nucleic Acids Res. 2006 May 24;34(9):e70.PMID: 16723429 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.

Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD.

PLoS One. 2009;4(3):e4702. Epub 2009 Mar 11.PMID: 19277110 [PubMed - indexed for MEDLINE]Related articlesFree article

Robust detection and genotyping of single feature polymorphisms from gene expression data.

Wang M, Hu X, Li G, Leach LJ, Potokina E, Druka A, Waugh R, Kearsey MJ, Luo Z.

PLoS Comput Biol. 2009 Mar;5(3):e1000317. Epub 2009 Mar 13.PMID: 19282978 [PubMed - indexed for MEDLINE]Related articlesFree article

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.

Toleno DM, Renaud G, Wolfsberg TG, Islam M, Wildman DE, Siegmund KD, Hacia JG.

BMC Bioinformatics. 2009 Mar 5;10:77.PMID: 19265541 [PubMed - indexed for MEDLINE]Related articlesFree article

A multivariate prediction model for microarray cross-hybridization.

Chen YA, Chou CC, Lu X, Slate EH, Peck K, Xu W, Voit EO, Almeida JS.

BMC Bioinformatics. 2006 Mar 1;7:101.PMID: 16509965 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene set enrichment analysis for non-monotone association and multiple experimental categories.

Lin R, Dai S, Irwin RD, Heinloth AN, Boorman GA, Li L.

BMC Bioinformatics. 2008 Nov 14;9:481.PMID: 19014579 [PubMed - indexed for MEDLINE]Related articlesFree article

An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.

Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, Shimizu H, Yomo T.

Bioinformatics. 2008 May 15;24(10):1278-85. Epub 2008 Mar 31.PMID: 18378525 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

Yao J, Chang C, Salmi ML, Hung YS, Loraine A, Roux SJ.

BMC Bioinformatics. 2008 Jun 18;9:288.PMID: 18564431 [PubMed - indexed for MEDLINE]Related articlesFree article

Modeling of DNA microarray data by using physical properties of hybridization.

Held GA, Grinstein G, Tu Y.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7575-80. Epub 2003 Jun 13.PMID: 12808153 [PubMed - indexed for MEDLINE]Related articlesFree article

Empirical Bayes models for multiple probe type microarrays at the probe level.

Astrand M, Mostad P, Rudemo M.

BMC Bioinformatics. 2008 Mar 20;9:156.PMID: 18366694 [PubMed - indexed for MEDLINE]Related articlesFree article

A new method for class prediction based on signed-rank algorithms applied to Affymetrix microarray experiments.

Rème T, Hose D, De Vos J, Vassal A, Poulain PO, Pantesco V, Goldschmidt H, Klein B.

BMC Bioinformatics. 2008 Jan 11;9:16.PMID: 18190711 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequence dependence of cross-hybridization on short oligo microarrays.

Wu C, Carta R, Zhang L.

Nucleic Acids Res. 2005 May 24;33(9):e84.PMID: 15914663 [PubMed - indexed for MEDLINE]Related articlesFree article