29.2.14. Array LIMS - arrays

Figure 29.15. Array LIMS - arrays

Array LIMS - arrays

Array designs

Array designs are stored in ArrayDesignData objects and can be created either as standalone designs or from plates. In the first case the features on an array design are described by a reporter map. A reporter map is a file that maps a coordinate (block, meta-grid, row, column), position or an external ID on an array design to a reporter. Which method to use is given by the ArrayDesign.featureIdentificationMethod property. The coordinate system on an array design is divided into blocks. Each block can be identified either by a blockNumber or by meta coordinates. This information is stored in ArrayDesignBlockData items. Each block contains several FeatureData items, each one identified by a row and column coordinate. Platforms that doesn't divide the array design into blocks or doesn't use the coordinate system at all must still create a single super-block that holds all features.

Array designs that are created from plates use a print map file instead of a reporter map. A print map is similar to a plate mapping but maps features (instead of wells) to wells. The file should specifify which plate and well a feature is created from. Reporter information will automatically be copied by BASE from the well.

It is also possible to skip the importing of features into the database and just keep the data in the orginal files instead. This is typically done for Affymetrix CDF files.

Array slides

The ArraySlideData represents a single array. Arrays are usually printed several hundreds in a batch, represented by a ArrayBatchData item. The batchIndex is the ordinal number of the array in the batch. The barcode can be used as a means for external programs to identify the array. BASE doesn't care if a value is given or if they are unique or not. If the destroyed flag is set it prevents a slide from beeing used by a hybridization.