Table of Contents
This chapter will explain the important features of BASE.
BASE supports many different vendor specific and custom printing microarray platforms and data formats, there are even users that use BASE for protein arrays. For 2 channel array platforms it is straightforward to customize BASE for a specific array platform, the platform simply needs to be adapted to the (BASE) Generic platform. The adaptation is to create a raw data format definition and to configure raw data importers, or make use of already available raw data formats. However, it is not always possible to make an natural mapping of a platform to the Generic platform. Platforms such as Affymetrix and Illumina platforms cannot naturally be mapped on to the Generic 2 channel platform. For Affymetrix, BASE comes with a specific Affymetrix platform and Illumina can be supported by customizing BASE.
How to adapt new array platforms to the Generic platform format or how to create a new platform type in BASE can be read elsewhere in this document. Here we list different array platforms used in BASE and also list raw data types supported by BASE. However, not all platforms nor raw data types listed below are available out-of-the box and a BASE administrator must customize his local BASE installation for their specific need. What comes pre-configured when BASE is installed is indicated in the lists below.
Not all array platforms listed below are available by default. The comments to specific platforms explain how to enable the use of the array platform in BASE. In some cases there is no confirmed usage of a platform but we believe it has been tested by anonymous users.
The Affymetrix platform comes pre-configured with a new BASE installation. Affymetrix platform in this context are the Affymetrix expression arrays. So far there has been no reason for expanding the Array platform to other chip-types. In principle any Affymetrix chip type can be stored in BASE but current plug-ins will always assume that expression data is stored and analyzed. This can be resolved by adding variants of the Affymetrix platform but the Lund BASE team currently has no plans to create Affymetrix variants.
The array layout options are endless and imagination is the only limitation ... almost. BASE can import many in-house array designs and platforms. The custom arrays usually fall back on one of the raw data types already available such as GenePix.
There are several variants of the Illumina platform. Using several variants allows BASE to adapt its handling of different Illumina chip types. Illumina platform support is not included in a standard BASE installation but there is a Illumina plug-in available for seamless integration of the Illumina array platform to BASE.
No successful use confirmed but ImaGene raw data is available in BASE.
In principle any platform generating a matrix of data can be imported into BASE. Simply utilize the available raw data formats and data importers.
Raw data comes in many different formats. These formats are usually defined by scanner software vendors and BASE must keep track of the different formats for analysis and plotting. BASE supports many formats out the box, but some formats need to be added manually by the BASE administrator (indicated in the list below).
The Illumina array platform usage is recommended to be based on the Illumina Bead Summary (IBS) raw data format below.
Not available in BASE directly but it is added with the Illumina plug-in that adds Illumina array platform support to BASE.