2.2.4.2.1 Array properties

The following tags are mandatory:

<Organism> :

species

<Project> :

project name

<Name> :

array name

<Type> :

array type. Any type description may be used, but default VAMP functions are associated with the following types: CGH, Trs, LOH, SNP, and ChIP, as described in table 2.1

<Ratio> :

the type of the signal value: ratio (M) or log ratio (L).

<Url> :

the physical localization of the XML files which contains the array data for each chromosome (tag <Chr>); these Urls are used by the software for saving analysis (save command of File menu) and restore any saved analysis (load command of the File menu).

The following tags are optional, but filling them allows one to identify the patient, and therefore to link together profiles from the same patient, e.g. array-CGH and transcriptome data:

<ProjectId> :

identification of the project

<NumHisto> :

histological number (which corresponds to a unique patient ID)

The tag <SampleAdditionalData> links array files with additional data (e.g. clinical data) that are stored for a given sample in an XML file, as described in section 2.2.4.

Any other tag may be added in the <Array> description. They will be listed in the Info Panel of the bottom-left frame (figure 3.3), and will be taken into account by the Search Arrays function (section 3.2.3).