12.1. Platforms

12.1.1. Platform variants

An experimental platform in BASE can be seen as an item representing the set of data file types that are produced or needed by a given experimental setup. For example, the Affymetrix platform (as defined in BASE) uses CEL files for raw data and CDF files for array design information.

The concept of a platform is also tightly coupled to the ability to keep data in files instead of importing it to the database. When you have selected a platform for a raw bioassay or an array design, you also know which files you should provide.

BASE comes pre-installed with two platforms; A generic platform and the Affymetrix platform. Other platforms, such as Illumina, are available as non-core plug-in packages, see Section 4.3, “BASE plug-ins site”. An administrator may define additional platforms and file types.

You can manage platforms going to AdministratePlatformsExperimental platforms.

Figure 12.1. Platform properties

Platform properties


The name of the platform

External ID

An ID that is used to identify the platform. The ID must be unique and can't be changed once the platform has been created.


If the platform is a file-only platform or not. File-only platforms can't have it's data imported into the database. This option can't be changed once the platform has been created.

Raw data type

If you have selected file-only=no, you may select a raw data type. This will lock this platform to the selected raw data type. If you select - any -, raw data of any raw data type can be used. This option can't be changed once the platform has been created.


If you have selected file-only=yes, you must enter the number of channels the platform uses. This information is needed in the analysis module of BASE to create the proper database tables. This option can't be changed once the platform has been created.


A description of the platform.

Figure 12.2. Select data file types

Select data file types

Data file types

This list contains the file types already associated with this platform. An [x] at the end of the name indicates a required file.


This checkbox will modify the required flag for the selected file types.

[Note] Note

The requried flag is not a hard requirement. It is only used for generating warnings when validating an experiment.

Add data file types

Opens a popup window that allows you to add more file types to the platform.


Removes the selected file types from the platform.

12.1.1. Platform variants

It is possible for an administrator to define variants of a platform. The main purpose for this is to be able to select additional file types that are only used in some cases. The file types defined by the parent platform are always inherited by the variants.

You can create new variants from the single-item view of a platform. This view also has a Variants tab which lists all variants that has been defined for a platform.