Potential bias in GO::TermFinder. Export

@article{citeulike:4173043, abstract = {The increased need for multiple statistical comparisons under conditions of non-independence in bioinformatics applications, such as DNA microarray data analysis, has led to the development of alternatives to the conventional Bonferroni correction for adjusting P-values. The use of the false discovery rate (FDR), in particular, has grown considerably. However, the calculation of the FDR frequently depends on drawing random samples from a population, and inappropriate sampling will result in a bias in the calculated FDR. In this work, we demonstrate a bias due to incorrect random sampling in the widely used GO::TermFinder package. Both T(2) and permutation tests are used to confirm the bias for a test set of data, which leads to an overestimation of the FDR of about 10\%. A simple fix to the random sampling method is proposed to remove the bias.}, author = {Flight, Robert M. and Wentzell, Peter D.}, citeulike-article-id = {4173043}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bib/bbn054}, citeulike-linkout-1 = {http://bib.oxfordjournals.org/content/bbn054/.abstract}, citeulike-linkout-2 = {http://bib.oxfordjournals.org/content/bbn054/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19279157}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19279157}, day = {1}, doi = {10.1093/bib/bbn054}, issn = {1477-4054}, journal = {Briefings in bioinformatics}, keywords = {gene\_ontology, gene\_set\_analysis}, month = {May}, number = {3}, pages = {289--294}, posted-at = {2009-11-04 11:15:47}, priority = {2}, title = {Potential bias in GO::TermFinder.}, url = {http://dx.doi.org/10.1093/bib/bbn054}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:4173043 L3 - citeulike-article-id:4173043 N2 - The increased need for multiple statistical comparisons under conditions of non-independence in bioinformatics applications, such as DNA microarray data analysis, has led to the development of alternatives to the conventional Bonferroni correction for adjusting P-values. The use of the false discovery rate (FDR), in particular, has grown considerably. However, the calculation of the FDR frequently depends on drawing random samples from a population, and inappropriate sampling will result in a bias in the calculated FDR. In this work, we demonstrate a bias due to incorrect random sampling in the widely used GO::TermFinder package. Both T(2) and permutation tests are used to confirm the bias for a test set of data, which leads to an overestimation of the FDR of about 10%. A simple fix to the random sampling method is proposed to remove the bias. IS - 3 JF - Briefings in bioinformatics SN - 1477-4054 EP - 294 TI - Potential bias in GO::TermFinder. VL - 10 SP - 289 KW - gene_ontology KW - gene_set_analysis AU - Flight, Robert AU - Wentzell, Peter PY - 2009/05/01/ UR - http://dx.doi.org/10.1093/bib/bbn054 ER -