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Working with datasets

The dataset view is the 'home page' for the uploaded dataset. It provides information about the dataset, allows you to run analyses and gives the status of submitted jobs (figure 1). The sections below give more details about the available functionality on this page.

The dataset page

Figure 1: The dataset page

[Top]Accessing a dataset

To access an uploaded dataset, unregistered (anonymous) users will need to visit the web address of the dataset's page, which is can be saved (e.g. bookmarked) during the upload process. Registered users have a list of their datasets on the My datasets page, and can access a particular dataset by clicking on its name.

[Top]'About this dataset' panel

'About this dataset' panel

Figure 2: The About this dataset panel

The panel on the right hand side of the dataset page gives information about the dataset, allows editing of the dataset's notes and enables attachment of survival data (figure 2), and downloading of the TMA data and survival data, if previously uploaded. The information listed in the panel is as follows:

Editing the dataset's notes

To edit the notes on a dataset, click directly on the notes, or on the message 'Click here to edit'. A text box appears in the notes area allowing editing. When complete, click on the save button. Clicking on the cancel button, or elsewhere on the page, will discard any changes.

Attaching survival data

Attach survival button highlighted on the dataset page

Figure 3: The dataset page with the Attach survival button highlighted.

Dialog box to attach survival data to a TMA dataset

Figure 4: Dialog for attaching survival data to a TMA dataset

Survival data is required to perform certain types of analyses - Kaplan-Meier plots of marker scores against survival, for example. Please refer to formatting requirements for the survival file to prepare the data.

Once you have a file ready for upload, go the dataset view for the relevant dataset, and click the Attach survival button. The button is located in the About this dataset panel on the right-hand side (figure 3). A dialog box will then appear (figure 4). Click on Upload a file and select the survival file on your computer. After a few moments, the survival file will be uploaded and subject to validation. If the file validates successfully, a confirmation box will appear stating that survival data has been attached. If the file does not validate, an error message will be displayed, and there will be the opportunity to upload a new file after correcting any issues raised in the error message.

[Top]Running analyses

The 'Run analysis' dialog

Figure 5: The Run analysis dialog with the Mixture model plots analysis selected

To choose an analysis, click the Run analysis button at the top left of the dataset page. A dialog box will then appear allowing you to choose an analysis (figure 5). On the left is a list of available analyses, the right side gives information about the selected analysis. The list of analysis categories shows the name of each category, followed by the number of available analyses in brackets. Click on an analysis category, for example Data exploration, and a list of analyses in that category will appear below. Selecting an analysis from the list gives a summary of the analysis on the right-hand side. To select an alternative analysis, use the list on the left hand side. For more information on the selected analysis, click the Help button on the top right.

To start the selected analysis, click the Run analysis button in the dialog box (Figure 5). After a few moments, the box will close and the job will be added to the Pending analyses table at the bottom of the page. Once the analysis has finished, it will move from the Pending analyses table to the Completed analyses table.

To view the results of an analysis, click on its name in the Completed analyses table.

If an error occurs running an analysis, the message Error, with a Help button next to it, will appear under Completion date. Click on the button for more information on why the analysis was unable to run, which is often due to the specifics of the dataset.

[Top]Pending analyses

The 'Pending analyses' table

Figure 6: The 'Pending analyses' table, which shows analyses currently being processed or in a queue

Pending analyses are shown in a table (figure 6) beneath any completed analyses. If there are no analyses currently queued or processing, a message is displayed to that effect.

Pending analyses are listed in the table with the following information:

[Top]Completed analyses

The 'Completed analyses' table

Figure 7: The 'Completed analyses' table

The completed analyses table (figure 7) shows a list of analyses that have been processed, grouped by category. To view the results of a successful analysis, click on its name. For more information on interpreting results, see analysis types.

The table contains the following information:

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