Statistical Applications in Genetics and Molecular Biology
Editor-in-Chief: Sanguinetti, Guido
IMPACT FACTOR 2018: 0.536
5-year IMPACT FACTOR: 0.764
CiteScore 2018: 0.49
SCImago Journal Rank (SJR) 2018: 0.316
Source Normalized Impact per Paper (SNIP) 2018: 0.342
Mathematical Citation Quotient (MCQ) 2018: 0.02
Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study
The level of differential gene expression may be defined as a fold change, a frequency of upregulation, or some other measure of the degree or extent of a difference in expression across groups of interest. On the basis of expression data for hundreds or thousands of genes, inferring which genes are differentially expressed or ranking genes in order of priority introduces a bias in estimates of their differential expression levels. A previous correction of this feature selection bias suffers from a lack of generality in the method of ranking genes, from requiring many biological replicates, and from unnecessarily overcompensating for the bias.For any method of ranking genes on the basis of gene expression measured for as few as three biological replicates, a simple leave-one-out algorithm corrects, with less overcompensation, the bias in estimates of the level of differential gene expression. In a microarray data set, the bias correction reduces estimates of the probability of upregulation or downregulation from 100% to as low as 60%, even for genes with estimated local false discovery rates close to 0. A simulation study quantifies both the advantage of smoothing estimates of bias before correction and the degree of overcompensation.
Keywords: conditional bias; conditionally biased estimation; feature selection bias; shrinkage; empirical Bayes; gene rank; data resampling; transcriptional microarray; differential gene expression; fold change estimation; multiple comparisons; cross validation
Hier finden Sie eine Übersicht über alle Crossref-gelisteten Publikationen, in denen dieser Artikel zitiert wird. Um automatisch über neue Zitierungen dieses Artikels informiert zu werden, aktivieren Sie einfach oben auf dieser Seite den „E-Mail-Alert: Neu zitiert“.