MOTIVATION: In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger 'pseudolibraries'. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation. RESULTS: We introduce a beta-binomial sampling model that correctly incorporates both sources of variation. We show how to fit the parameters of this model, and introduce a test statistic for differential expression similar to a two-sample t-test.
MOTIVATION: In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger 'pseudolibraries'. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation. RESULTS: We introduce a beta-binomial sampling model that correctly incorporates both sources of variation. We show how to fit the parameters of this model, and introduce a test statistic for differential expression similar to a two-sample t-test.
Authors: Morgan M Steffen; B Shafer Belisle; Sue B Watson; Gregory L Boyer; Richard A Bourbonniere; Steven W Wilhelm Journal: Appl Environ Microbiol Date: 2015-02-06 Impact factor: 4.792
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Authors: Sanggyu Lee; Jianjun Chen; Guolin Zhou; Run Zhang Shi; Gerard G Bouffard; Masha Kocherginsky; Xijin Ge; Miao Sun; Nimanthi Jayathilaka; Yeong Cheol Kim; Neelmini Emmanuel; Stefan K Bohlander; Mark Minden; Justin Kline; Ozden Ozer; Richard A Larson; Michelle M LeBeau; Eric D Green; Jeffery Trent; Theodore Karrison; Piu Paul Liu; San Ming Wang; Janet D Rowley Journal: Proc Natl Acad Sci U S A Date: 2006-01-17 Impact factor: 11.205
Authors: Lauren A Sugden; Michael R Tackett; Yiannis A Savva; William A Thompson; Charles E Lawrence Journal: Bioinformatics Date: 2013-09-17 Impact factor: 6.937