The following links load some of the above data sets and allow you to start an actual run of Pomelo II. You do need to select the options yourself; we only load the data.
Contingency table example. Analyze using "Fisher IxJ" options under Test.
Leukemia example. Analyze using a permutation t-test or a t-test with limma.
Srbct example. A linear model with four classes. You must select Anova linear models test (under Test options) and select "Continue without covariables" in the second input screen.
Breast example. A linear model with three classes and additional covariates. You must select Anova linear models test (under Test options), and select "Send covariables" in the second input screen. In the third screen, select whichever covariables you want.
An example with censored survival data. You must select Cox model (under Test options).
This is a survival data example with very little signal. By default, the results show no heatmap, but of course you can change the options and draw a heatmap. The heatmap and table both are clickable and will give you more data on the genes, based on the IDConverter databases. (These are the same data as used in the Named Genes example of signs.)
Here you can examine the sets of GO terms, KEGG and Reactome pathways, and PubMed references in the set of selected genes (you choose the criteria for selection). Scroll to the bottom of the page, and click the "Send genes to PaLS", to be taken to a screen where you select the criteria for sending the genes for PaLS analysis.
The data for the Fisher's test example are fictitious. Details on the data sets Leukemia, Srbc and Breast, including their origin and preprocessing are available from the supplementary material to the paper Gene selection and classification of microarray data using random forest. The additional covariates for the Srbct example are fictitious.
The text of this document and the comments added to the output are copyright © 2005-2009 Ramón Díaz-Uriarte. You can, however, do quite a bit of things with all the text, since this document is licensed under a Creative Commons license, as shown below (click on the links to read the terms of the license).