Limits...
EPEPT: a web service for enhanced P-value estimation in permutation tests.

Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I - BMC Bioinformatics (2011)

Bottom Line: Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values.Finally, the source code of EPEPT can be downloaded.Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology, Seattle, WA, USA. tknijnenburg@systemsbiology.org

ABSTRACT

Background: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values.

Results: The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded.

Conclusions: Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

Show MeSH
Example R code to run EPEPT. The inputs (including the tab delimited text file 'mytestdata.tsv' that contains the permutation values) are submitted by making a request to EPEPT after which a unique URI is returned to the client. Using this URI the status of the submitted job can be checked. When the job is completed, the estimated P-values are retrieved using the URI and stored in variable P.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3277916&req=5

Figure 4: Example R code to run EPEPT. The inputs (including the tab delimited text file 'mytestdata.tsv' that contains the permutation values) are submitted by making a request to EPEPT after which a unique URI is returned to the client. Using this URI the status of the submitted job can be checked. When the job is completed, the estimated P-values are retrieved using the URI and stored in variable P.

Mentions: Figure 4 presents a small example, where R is employed to run EPEPT. The EPEPT website http://informatics.systemsbiology.net/EPEPT/ provides examples for four programming languages (R, Perl, MATLAB and Ruby) and offers downloads to the libraries necessary to run these examples. Also, test data sets and documentation on the exact input requirements (i.e. the variable names to be used) are available.


EPEPT: a web service for enhanced P-value estimation in permutation tests.

Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I - BMC Bioinformatics (2011)

Example R code to run EPEPT. The inputs (including the tab delimited text file 'mytestdata.tsv' that contains the permutation values) are submitted by making a request to EPEPT after which a unique URI is returned to the client. Using this URI the status of the submitted job can be checked. When the job is completed, the estimated P-values are retrieved using the URI and stored in variable P.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3277916&req=5

Figure 4: Example R code to run EPEPT. The inputs (including the tab delimited text file 'mytestdata.tsv' that contains the permutation values) are submitted by making a request to EPEPT after which a unique URI is returned to the client. Using this URI the status of the submitted job can be checked. When the job is completed, the estimated P-values are retrieved using the URI and stored in variable P.
Mentions: Figure 4 presents a small example, where R is employed to run EPEPT. The EPEPT website http://informatics.systemsbiology.net/EPEPT/ provides examples for four programming languages (R, Perl, MATLAB and Ruby) and offers downloads to the libraries necessary to run these examples. Also, test data sets and documentation on the exact input requirements (i.e. the variable names to be used) are available.

Bottom Line: Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values.Finally, the source code of EPEPT can be downloaded.Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology, Seattle, WA, USA. tknijnenburg@systemsbiology.org

ABSTRACT

Background: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values.

Results: The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded.

Conclusions: Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

Show MeSH