29.2.16. Hybridizations and raw data

UML diagram

Figure 29.17. Hybridizations and raw data

Hybridizations and raw data


Hybridizations connects the slides from the Array LIMS part with labeled extracts from the biomaterials part. The creationEvent is used to register which labeled extracts that were used on the hybridization. The relation to slides is a one-to-one relation. A slide can only be used on a single hybridization and a hybridization can only use a single slide. The relation is optional from both sides.

The scanning of the hybridized slide is registered as separate scan events. One or more images can optionally be attached to each scan. The images are not used by BASE.

Raw data

A RawBioAssayData object represents the raw data that is produced by analysing the image(s) from a single scan. You may register which software that was used, the protocol and any parameters (through the annotation system).

Files with the analysed data values can be attached to the associated FileSetData object. The platform and, optionally, the variant has information about the file types that can be used for that platform. If the platform file types support metadata extraction, headers, the number of spots, and other information may be automatically extracted from the raw data file(s).

If the platform support it, raw data can also be imported into the database. This is handled by batchers and RawData objects. Which table to store the data in depends on the rawDataType property. The properties shown for the RawData class in the diagram are the mandatory properties. Each raw data type defines additional properties that are specific to that raw data type.

Spot images

Spot images can be created if you have the original image files. BASE can use 1-3 images as sources for the red, green and blue channel respectively. The creation of spotimages requires that x and y coordinates are given for each raw data spot. The scaling and offset values are used to convert the coordinates to pixel coordinates. With this information BASE is able to cut out a square from the source images that, theoretically, contains a specific spot and nothing else. The spot images are gamma-corrected independently and then put together into PNG images that are stored in a zip file.