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EntropyExplorer: an R package for computing and comparing differential Shannon entropy, differential coefficient of variation and differential expression.

Wang K, Phillips CA, Saxton AM, Langston MA - BMC Res Notes (2015)

Bottom Line: Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data.No standard method was found to be appropriate for DSE, and so permutation testing is used to calculate DSE p values.EntropyExplorer provides a convenient resource for calculating DSE, DCV, DE and associated p values.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996-2250, USA. kwang11@tennessee.edu.

ABSTRACT

Background: Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data. They can serve to augment differential expression (DE), and be applied in numerous settings whenever one seeks to measure differences in variability rather than mere differences in magnitude. A general purpose, easily accessible tool for DSE and DCV would help make these two metrics available to data scientists. Automated p value computations would additionally be useful, and are often easier to interpret than raw test statistic values alone.

Results: EntropyExplorer is an R package for calculating DSE, DCV and DE. It also computes corresponding p values for each metric. All features are available through a single R function call. Based on extensive investigations in the literature, the Fligner-Killeen test was chosen to compute DCV p values. No standard method was found to be appropriate for DSE, and so permutation testing is used to calculate DSE p values.

Conclusions: EntropyExplorer provides a convenient resource for calculating DSE, DCV, DE and associated p values. The package, along with its source code and reference manual, are freely available from the CRAN public repository at http://cran.r-project.org/web/packages/EntropyExplorer/index.html.

No MeSH data available.


Related in: MedlinePlus

Another use of EntropyExplorer on breast cancer data. The function call has specified “dcv” for differential coefficient of variation, “bv” to specify both value and p value, and to sort by value, and 12 to return the top 12 rows
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Fig2: Another use of EntropyExplorer on breast cancer data. The function call has specified “dcv” for differential coefficient of variation, “bv” to specify both value and p value, and to sort by value, and 12 to return the top 12 rows

Mentions: We refer the reader to the reference manual, included as Additional file 1 and available on the project webpage, for a detailed description of all arguments and options. Included with the package is a sample mRNA microarray dataset, consisting of a few rows from a dataset obtained from the Gene Expression Omnibus (GEO) [17]. This dataset, GSE10810, contains case/control data on breast cancer [18]. Figures 1 and 2 provide example uses of EntropyExplorer on the full data.Fig. 1


EntropyExplorer: an R package for computing and comparing differential Shannon entropy, differential coefficient of variation and differential expression.

Wang K, Phillips CA, Saxton AM, Langston MA - BMC Res Notes (2015)

Another use of EntropyExplorer on breast cancer data. The function call has specified “dcv” for differential coefficient of variation, “bv” to specify both value and p value, and to sort by value, and 12 to return the top 12 rows
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696313&req=5

Fig2: Another use of EntropyExplorer on breast cancer data. The function call has specified “dcv” for differential coefficient of variation, “bv” to specify both value and p value, and to sort by value, and 12 to return the top 12 rows
Mentions: We refer the reader to the reference manual, included as Additional file 1 and available on the project webpage, for a detailed description of all arguments and options. Included with the package is a sample mRNA microarray dataset, consisting of a few rows from a dataset obtained from the Gene Expression Omnibus (GEO) [17]. This dataset, GSE10810, contains case/control data on breast cancer [18]. Figures 1 and 2 provide example uses of EntropyExplorer on the full data.Fig. 1

Bottom Line: Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data.No standard method was found to be appropriate for DSE, and so permutation testing is used to calculate DSE p values.EntropyExplorer provides a convenient resource for calculating DSE, DCV, DE and associated p values.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996-2250, USA. kwang11@tennessee.edu.

ABSTRACT

Background: Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data. They can serve to augment differential expression (DE), and be applied in numerous settings whenever one seeks to measure differences in variability rather than mere differences in magnitude. A general purpose, easily accessible tool for DSE and DCV would help make these two metrics available to data scientists. Automated p value computations would additionally be useful, and are often easier to interpret than raw test statistic values alone.

Results: EntropyExplorer is an R package for calculating DSE, DCV and DE. It also computes corresponding p values for each metric. All features are available through a single R function call. Based on extensive investigations in the literature, the Fligner-Killeen test was chosen to compute DCV p values. No standard method was found to be appropriate for DSE, and so permutation testing is used to calculate DSE p values.

Conclusions: EntropyExplorer provides a convenient resource for calculating DSE, DCV, DE and associated p values. The package, along with its source code and reference manual, are freely available from the CRAN public repository at http://cran.r-project.org/web/packages/EntropyExplorer/index.html.

No MeSH data available.


Related in: MedlinePlus