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).

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.

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

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:

Title: A title for the file. This is for your own reference. The maximum length is 48 characters.
Notes: (optional) Any notes you may wish to make about the dataset, again for your own reference, and can be edited later.
Scoring type: Categorical or continuous. A dataset is categorical when scores are in a small number of discrete categories (nine or fewer), e.g. using the Allred scoring system. Continuous datasets have scores which can take any value within a given range. Typically, the scoring type is automatically detected during the file validation stage and therefore can't be changed. The exception is small datasets where the scoring system can't be reliably identified. Please note that whole number scores should be used for categorical scoring. Currently, categorical data with more than nine scores are not supported - they will be treated as continuous. For such datasets, consider grouping score values together to produce nine or fewer different values, which will then be detected as categorical.
Batch correction: (datasets with continuous values and multiple batches only) This setting is used to indicate if batch correction is required. Batch correction is performed using the ComBat algorithm [Johnson et al. 2007 Biostatistics 8:118].
Replicate aggregation: (datasets with marker replicates only) This setting defines how scores for multiple replicates are combined to give a single score for a particular marker and patient. The available settings are mean and median. Mean is not available on datasets with categorical scoring. For more information on specifying replicates in datasets see data requirements - marker scores.

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:

Name - The name of the dataset, as entered during upload. Click the name to view the dataset.
Date uploaded - The date and time (GMT) when the dataset was uploaded to TMA Navigator.
Status - The current status of the dataset, indicating whether the dataset is ready for use.
- Queued - The dataset is in a queue waiting to be imported, and is not yet ready for analysis.
- Processing - The dataset is currently being imported and should be ready for analysis shortly.
- Ready - The dataset is ready for analysis. Click on the dataset name under the Name column to view the result.
- Validation error or Import error - An issue occurred during the import of the dataset which means it cannot be used. Click on the dataset's name to show a more detailed error message which provides some information to help with addressing the problem. See also the help section on error messages.
Delete - A button to delete the dataset and any associated analyses. See deleting a dataset.

[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.

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.