1 Detailed explanation

For a detailed manual for this section please access these links:

2 Menu: Clinical analysis

2.1 Sub-menu: Survival plot

Users can access the clinical data download in the TCGA data menu to verify the survival of different groups.

Survival plot menu: Main window.

2.1.1 Data

A csv or R object (rda) file with the clinical information.

2.1.2 Parameters

Group column: Select the column that identifies the group of each sample.
Legend text: Text of the legend.
Title: Title text.
x-axis limit: Limits the x-axis. If 0, no cut-off is considered.
Add p-value: Add p-value to the plot.

2.1.3 Size control

Changes the size of the plot

3 Menu: Manage summarized Experiment object

To facilitate visualization and modification of the SummarizedExperiment object, we created this menu in which it is possible to visualize the three matrices of the object (assay matrix [i.e. gene expresssion values], features matrix [i.e. gene information] and sample information matrix). Also, it is possible to download the sample information matrix as a csv file, and, after modifying it, to upload and update the SummarizedExperiment object. This might be useful if for example the user wants to compare two groups not already pre-defined.

Tutorial Video: Managing a SummarizedExperiment object - (http://www.youtube.com/watch?v=54NBug9ycwM)

4 Menu: Epigenetic analysis

4.1 Sub-menu: Differential methylation analysis

The user will be able to perform a Differential methylation regions (DMR) analysis. The output will be a file with the following pattern: DMR_results_GroupCol_group1_group2_pcut_1e-30_meancut_0.55.csv Also, the summarized Experiment will be saved with all the results inside it and the new object will be saved with _result suffix.

Obs: Depending on the number of samples and the number of probes of interest, this analysis can last anywhere from minutes to days. Duration of the analysis also depends on the type of machine and hardware on which it is run.