2.2.4.2.2 Object properties

Object descriptions are encapsulated as follows:

        <Obj>
            <Properties>
                 <Type>
                     // Obj Type
                 </Type>
                 // other Obj Properties
            </Properties>
        </Obj>

Tag <Type> describes the object type. Any type description may be used, but the default VAMP functions are associated to the following types : Clone, Probeset, Microsat, SNP, and Probe.

There is a default type for the objects of an array, which depends on the array type as summarized in Table 2.1.

Table 2.1: Default object types in the different types of arrays

Data type	Array type	Object type
CGH-array	CGH	Clone
transcriptome arrays	Trs	ProbeSet
Loss Of Heterozygosity data	LOH	Microsat
Single Nucleotide Polymorphism arrays	SNP	SNP
Chromatine ImmunoPrecipitation arrays	ChIP	Probe

Any XML tag may be used for describing objects in VAMP, but some of them are mandatory. Some others are required to use some of the VAMP functions. The list of mandatory or required object tags depends on the array type. In the two following paragraphs we describe the mandatory and optional tags we used for the two most widely used data: array-CGH data and transcriptome array data.