RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
This work is about assessing model adequacy for negative binomial (NB) regression, particularly
(1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness
of models for NB dispersion parameters. Tools for the first are appropriate for NB
regression generally; those for the second are primarily intended for...
Full Text:
Model
Diagnostics for Negative Binomial Regression of RNA
Sequencing Data
Gu Mi1,*, Yanming Di1,2
This work is about assessing model adequacy for negative binomial (NB) regression, particularly
(1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness
of models for NB dispersion parameters. Tools for the first are appropriate for NB
regression generally; those for the second are primarily intended for...
Full Text:
Negative Binomial
Regression of RNA Sequencing Data
Mi, G., Di, Y., & Schafer, D. W. (2015). Goodness-of
This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for...
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
Full Text:
berries
Gouthu, S., O’Neil, S. T., Di, Y., Ansarolia, M., Megraw, M., & Deluc, L. G. (2014).
A
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and
quantifying gene expression changes. This next generation sequencing-based method provides unprecedented
depth and resolution. The negative binomial (NB) probability distribution has been shown to be a
useful model for frequencies of mapped RNA-Seq reads and consequently provides...
When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...