Plug-in download

This page provides easy access to BASE 1 and 2 plug-ins for users who prefer not to use the subversion repository for downloading the plug-ins

The latest stable BASE can be downloaded from the ​BASE 2 development site. The latest BASE 1 release is available from ​BASE 1.2.x development site and the latest ​BASE 1.2 plug-in development kit may be needed for some of the BASE 1 plug-ins.

BASE 2 plug-ins

Plug-ins created for BASE 2 do not work with BASE 1.x.

Quality Control (QC)

Transformation

Normalization

Affymetrix plug-in for BASE: Affymetrix normalization with RMAExpress or Plier (​download latest ​MD5). The Plier algorithm in this plug-in is superseded by the ​APT plug-in. Works with BASE 2.0 and later
​APT: Affymetrix Power Tools execution plug-in. Currently apt-probeset-summarize and apt-probeset-geneotype from APT is acccessible through this plug-in. Works with BASE 2.4 and later

Filter

Analysis

Other

Illumina plug-ins package: A package of plug-ins for working with Illumina Sentrix and Illumina SNP arrays. Works with BASE 2.6 and later
BatchDataImporter: Imports batches of data files into BASE, creating a single RawbioAssay for each file. Works with BASE 2.2 and later
Tab2MageImporter: Imports raw data files and an experiment meta-data in the tab2mage specification into base 2. Works with BASE 2.2 and later
Tab2MageExporter: Exports an experiment meta-data in the tab2mage specification from base 2. Works with BASE 2.2 and later
AffyArrayDesignBatchImporter: Imports batches of affymetrix array design into base 2. Works with BASE 2.2 and later
AnnotationTypeCvImporter: Import annotation type annd controlled vocabularies from a simple flat file into base 2. Works with BASE 2.0 and later
GCRMA: Works with BASE 2.0 and later
BAFsegmentation: Segments B allele frequencies from SNP arrays to identify regions of allelic imbalance. Not released yet
WeNNI: Missing value imputation. Not released yet

BASE 1.2 plug-ins

Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plug-in.

Quality Control (QC)

Transformation

Merge BioAssay: Works with BASE 1.2.17+
Smooth: Works with BASE 1.2.17+
WeNNI: Missing value imputation (​download latest). Works with BASE 1.2.17+

Normalization

popLowess: Works with BASE 1.2.17+

Filter

Analysis

One class Z-test: Works with BASE 1.2.17+

Other

Example code

Plug-ins

Example plug-ins for BASE2: A package with example plug-ins intended for the developer. Works with BASE 2.6 and later

Web services

Web services examples for BASE 2: A package with a Java client application that uses web services to get information from a BASE 2 server. Works with BASE 2.6 and later

External BASE plug-in developer sites

The MicroArray Datawarehouse Resource@LCB develops BASE plug-ins, please visit their development site at ​http://madr.lcb.uu.se/.