It lists the accepted sorting methods for analysis results
It lists the p-value combining methods
It lists the supported GSEA methods. Since EGSEA base methods are implemented in the Bioconductor project, the most recent version of each individual method is always used.
This function writes out the official EGSEA package logo
1 2 3 4 5 6 7
character, the target directory to which the logo will be written.
These methods include:
ora, globaltest, plage, safe, zscore,
gage, ssgsea, roast, fry, padog,
camera and gsva.
ora, gage, camera and
gsva methods depend on a competitive null
hypothesis while the remaining seven methods are based on a self-contained hypothesis.
Conveniently, EGSEA is not limited to these twelve
GSE methods and new GSE tests can be easily integrated into the framework.
Note: the execution time of base methods can vary depending on the size of gene set collections, number of samples, number of genes and number of contrasts. When a gene set collection of around 200 gene sets was tested on a dataset of 17,500 genes, 8 samples and 2 contrasts, the execution time of base methods in ascending order was as follows:
globaltest; safe; gage; gsva; zscore; plage; fry; camera; ora; ssgsea; padog. When the
same dataset was tested on a large gene set collection of 3,700 gene sets, the execution
time of base methods in ascending order was as follows:
globaltest; camera; fry; zscore; plage; safe; gsva; ora; gage; padog; ssgsea. Apparently, the
size of gene set collection plays a key role in the execution time of most of the base
methods. The reduction rate of execution time between the large and small gene set
collections varied between 18% and 88%.
camera, fry, plage, zscore and
ora showed the least
reduction rate of execution time. As a result, there is no guarantee that a single combination
of base methods would run faster than other combinations. It is worth mentioning that
our simulation results showed that the increasing number of base methods in the EGSEA
analysis is desirable to achieve high performance.
This function generates a PNG file of the EGSEA logo, which can be used to acknowledge EGSEA in presentations/reports. The logo was designed by Roberto Bonelli from The Walter and Eliza Hall Institute of Medical Research.
It returns a character vector of the accepted values for the sort.by argument in egsea
It returns a character vector of available methods for the combineMethod argument in egsea
It returns a character vector of supported GSE methods.
a PNG file.
 Tavazoie, S. et al. (1999). Systematic determination of genetic network architecture.
Nature Genetics, 22(3), 281-5.
 Goeman, J. J. et al. (2004). A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20(1), 93-9.
 Tomfohr, J. et al. (2005). Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6, 225.
 Barry, W. T. et al. (2005). Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics, 21(9), 1943-9.
 Lee, E. et al. (2008). Inferring pathway activity toward precise disease classification. PLoS Computational Biology, 4(11), e1000217.
 Luo, W. et al. (2009). GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10, 161.
 Barbie, D. A. et al. (2009). Systematic RNA interference reveals that oncogenic KRASdriven cancers require TBK1. Nature, 462(7269), 108-12.
 Wu, D. et al. (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics, 26(17), 2176-82.
 Tarca, A. L. et al. (2009). A novel signaling pathway impact analysis. Bioinformatics, 25(1), 75-82.
 Wu, D. and Smyth, G. K. (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research, 40(17), e133.
 Hanzelmann, S. et al. (2013). GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics, 14, 7.
1 2 3 4 5
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.