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How to upload TMA data (registered users)

The process of uploading a dataset consists of two steps which are described in the sections below. Briefly, the first step is to supply a file containing marker values (typically TMA protein expression scores); the second step involves selecting options to be applied during the upload and providing information about the dataset (e.g. a title). Uploading and associated processing usually takes just a few moments. Registered users have access to a private My datasets page, containing a list of uploaded datasets and a facility to add new datasets. From here, the status of datasets can be viewed (if they are queued, processing or ready for analysis). The help section data requirements - marker scores gives information on how to organise your TMA data for successful uploading.

You can upload data using the Add dataset button on the top right of every page (figure 1).

The Add dataset button is present in the top right of the page (highlighted in red)

Figure 1: The Add dataset button (highlighted in red) is present on the top right of every page.

Stage 1: File validation

From the datasets page, click on the large Add dataset button (figure 2, highlighted in red).

You can also access the add dataset form from any page on the site by using the Add dataset button located in the set of buttons on the top right (figure 1, above). You will be redirected to the My datasets page once the file has been uploaded.

The 'My datasets' page, with the 'Add dataset' button highlighted in red

Figure 2: The My datasets page, with the Add dataset button highlighted in red.

The upload dataset form

Figure 3: The add dataset form, used to upload and annotate data.

With the add dataset form open (figure 3, above) click the button labelled Upload a file. You will then be asked to choose a file from your computer. Once you have selected a file, click OK. The file is then uploaded to the site and validated. The message Loading will appear with a progress bar. Please wait for the file to upload, even if the progress bar doesn't move. This process should only take a few moments.

Once the file is uploaded, it is validated (checked against data requirements). An error message is given if the dataset doesn't validate successfully - for example, if any scores are not numeric, or marker identifiers contain disallowed characters. If you get a validation error message there will be information included about how to modify your input data in order to pass validation. For details on the acceptable file formats and how to lay out your data, please see data requirements - marker scores. Please contact us if you require guidance on validating your data.

Stage 2: Data annotation and processing

The upload dataset form, filled in with annotation details and settings

Figure 4: The add dataset form, showing dataset annotation and settings.

Once the file has been validated successfully, you will be asked to enter a few details and select processing options (figure 4). The options on the form are as follows:

When the above has been completed, click the Save dataset button.

The dataset is then added to the dataset table (figure 5), which indicates its status (whether it is ready for use or not) and allows you to view the dataset and run analyses.

If an error occurs during import, the status will be listed as Validation error or Import error. Click the dataset name to view a more descriptive error message. For more information, see the help section dataset error messages.

[Top]The datasets page

The datasets table, with a dataset currently processing

Figure 5: The datasets table, shown with one dataset being imported (status reads 'Processing') and two datasets ready for analysis.

The datasets page displays the uploaded datasets in a table which lists datasets that you have uploaded, along with their status (Figure 5, above). There are four columns:

[Top]Accessing uploaded datasets

To view a dataset from the My datasets page, click on its name in the dataset table. For more information on the dataset view and running analyses, see working with datasets.

[Top]Deleting a dataset

Warning: Deleting a dataset will delete the dataset itself and any results associated with it. This action is irreversible.

The datasets table, with a dataset currently processing

Figure 6: A confirmation dialog shown after clicking 'Delete dataset'

To delete a dataset, click on the Delete button. A dialog box will ask you to confirm that you really want to delete the dataset (figure 6). Click the delete button on the dialog to proceed. After a short wait, the dataset will be deleted and removed from the datasets table - any results associated with the dataset will also be removed from TMA Navigator.

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