Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips Export

@article{citeulike:5397642, abstract = {Interlaboratory comparison of microarray data, even when using the same platform, imposes several challenges to scientists. RNA quality, RNA labeling efficiency, hybridization procedures and data-mining tools can all contribute variations in each laboratory. In Affymetrix GeneChips, about 11-20 different 25-mer oligonucleotides are used to measure the level of each transcript. Here, we report that labeling extension values (LEVs)', which are correlation coefficients between probe intensities and probe positions, are highly correlated with the gene expression levels (GEVs) on eukayotic Affymetrix microarray data. By analyzing LEVs and GEVs in the publicly available 2414 cel files of 20 Affymetrix microarray types covering 13 species, we found that correlations between LEVs and GEVs only exist in eukaryotic RNAs, but not in prokaryotic ones. Surprisingly, Affymetrix results of the same specimens that were analyzed in different laboratories could be clearly differentiated only by LEVs, leading to the identification of laboratory signatures'. In the examined dataset, GSE10797 , filtering out high-LEV genes did not compromise the discovery of biological processes that are constructed by differentially expressed genes. In conclusion, LEVs provide a new filtering parameter for microarray analysis of gene expression and it may improve the inter- and intralaboratory comparability of Affymetrix GeneChips data. 10.1093/nar/gkp168}, author = {Lee, Yun-Shien and Chen, Chun-Houh and Tsai, Chi-Neu and Tsai, Chia-Lung and Chao, Angel and Wang, Tzu-Hao}, citeulike-article-id = {5397642}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp168}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/37/8/e61.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/37/8/e61.full.pdf}, citeulike-linkout-3 = {http://www.ingentaconnect.com/content/oup/nar/2009/00000037/00000008/art00008}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19295132}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19295132}, day = {1}, doi = {10.1093/nar/gkp168}, issn = {0305-1048}, journal = {Nucl. Acids Res.}, keywords = {bias, microarray}, month = {May}, number = {8}, pages = {e61}, posted-at = {2009-11-05 23:34:49}, priority = {2}, publisher = {Oxford University Press}, title = {Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips}, url = {http://dx.doi.org/10.1093/nar/gkp168}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:5397642 L3 - citeulike-article-id:5397642 N2 - Interlaboratory comparison of microarray data, even when using the same platform, imposes several challenges to scientists. RNA quality, RNA labeling efficiency, hybridization procedures and data-mining tools can all contribute variations in each laboratory. In Affymetrix GeneChips, about 11-20 different 25-mer oligonucleotides are used to measure the level of each transcript. Here, we report that labeling extension values (LEVs)', which are correlation coefficients between probe intensities and probe positions, are highly correlated with the gene expression levels (GEVs) on eukayotic Affymetrix microarray data. By analyzing LEVs and GEVs in the publicly available 2414 cel files of 20 Affymetrix microarray types covering 13 species, we found that correlations between LEVs and GEVs only exist in eukaryotic RNAs, but not in prokaryotic ones. Surprisingly, Affymetrix results of the same specimens that were analyzed in different laboratories could be clearly differentiated only by LEVs, leading to the identification of laboratory signatures'. In the examined dataset, GSE10797 , filtering out high-LEV genes did not compromise the discovery of biological processes that are constructed by differentially expressed genes. In conclusion, LEVs provide a new filtering parameter for microarray analysis of gene expression and it may improve the inter- and intralaboratory comparability of Affymetrix GeneChips data. 10.1093/nar/gkp168 IS - 8 JF - Nucl. Acids Res. SN - 0305-1048 EP - e61 TI - Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips PB - Oxford University Press VL - 37 SP - e61 KW - bias KW - microarray AU - Lee, Yun-Shien AU - Chen, Chun-Houh AU - Tsai, Chi-Neu AU - Tsai, Chia-Lung AU - Chao, Angel AU - Wang, Tzu-Hao PY - 2009/05/01/ UR - http://dx.doi.org/10.1093/nar/gkp168 ER -