Question: How Do I Associate An Imported Array Design With An Experiment?
Topic: Working With Array Design Files
Release: v2.0 and above
Date entered: April 24, 2012
Answer
In caArray, before an experiment can be successfully created, the array design(s) for platforms used in that experiment have to be imported first. Afterwards, the array designs can be associated with the experiment in one of two ways.
Approach 1:
The most common way to associate the array designs is to select them when the experiment is created, as shown in Figure 1 below. By selecting array design(s) this way, you are telling caArray that the selected array design(s) correspond to the data files to be uploaded.
If only one array design is selected, caArray will associate all uploaded data files with that array design and will parse the data accordingly.
If more than one array design is selected, and if the data and sample annotations are in the MAGE-TAB format, additional information needs to be provided in the form of a SDRF metadata file in the CSV file format. In the SDRF file, which is a list of all the experiment's samples as shown in Figure 2 below, a column named “Array Design REF” (highlighted in red) shows the array design reference for each sample. This allows caArray to associate the correct array design with its corresponding array data files.
When entering the array design information into the SDRF file, be sure to pay attention to the syntax of the LSID reference. The correct reference syntax for most array designs supported by caArray can be found on the NCI instance of caArray at https://array.nci.nih.gov/caarray/home.action. Once you log in, you can click “Manage Array Designs”, then click on the array design that your data files use, and capture the value for “Array Design LSID”, as shown in Figure 3 below. Remember to remove the prefix “URN:LSID:” before you add the array design reference to the corresponding SDRF file column.
Approach 2:
A user can choose not to specify any array design when creating an experiment (notice that in Figure 1, the array design field on the web page is not marked by a red asterisk, meaning that field is not required). Instead, s/he can specify the array design(s) in a SDRF file as described above. Please pay attention to the syntax.
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