Adaptable gene-specific dye bias correction for two-channel DNA microarrays. Export

@article{citeulike:4493016, abstract = {DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA-bound proteins. DNA microarrays can suffer from gene-specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene- And Slide-Specific Correction, GASSCO) is presented, whereby sequence-specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence-based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.}, author = {Margaritis, Thanasis and Lijnzaad, Philip and van Leenen, Dik and Bouwmeester, Diane and Kemmeren, Patrick and van Hooff, Sander R. and Holstege, Frank C.}, citeulike-article-id = {4493016}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2009.21}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb200921}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19401678}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19401678}, day = {28}, doi = {10.1038/msb.2009.21}, issn = {1744-4292}, journal = {Molecular systems biology}, keywords = {bioconductor, dye\_bias, low\_level, microarray\_analysis, two-color}, month = {April}, posted-at = {2009-11-09 11:39:03}, priority = {0}, publisher = {EMBO and Nature Publishing Group}, title = {Adaptable gene-specific dye bias correction for two-channel DNA microarrays.}, url = {http://dx.doi.org/10.1038/msb.2009.21}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:4493016 L3 - citeulike-article-id:4493016 N2 - DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA-bound proteins. DNA microarrays can suffer from gene-specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene- And Slide-Specific Correction, GASSCO) is presented, whereby sequence-specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence-based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available. JF - Molecular systems biology SN - 1744-4292 TI - Adaptable gene-specific dye bias correction for two-channel DNA microarrays. PB - EMBO and Nature Publishing Group VL - 5 KW - bioconductor KW - dye_bias KW - low_level KW - microarray_analysis KW - two-color AU - Margaritis, Thanasis AU - Lijnzaad, Philip AU - van Leenen, Dik AU - Bouwmeester, Diane AU - Kemmeren, Patrick AU - van Hooff, Sander AU - Holstege, Frank PY - 2009/04/28/ UR - http://dx.doi.org/10.1038/msb.2009.21 ER -