Topic: caArray Usage
Release: Up to caArray 2.X
Date entered: 12/18/2009
One of the most frequently asked questions from the new caArray users is: "Where can I obtain the array design file for my experiment?". Although the array providers' websites are still the best places to obtain the most updated array design files (for more details, see caArray 010 - Where Are the Array Design Files for caArray? Where are the Array Design Files for caArray?), many array design files are now available to download at the NCI public caArray server, a new feature made available in caArray version 2.3.
In this KB entry, we will explain how to download, edit, delete and replace an array design file in caArray.
After login to caArray, the option to manage an array design will be available in the Curation section in the left menu. To select a file to download, follow the steps below:
Download of an existing array design file
Any registered caArray user can upload, validate, and import the array designs from a supported array provider. If a desired array design file is not found in the caArray, the user can initiate the file upload into caArray:
New Array Design Dialog with Form Completed
The required fields are the Description (Array Design test file in the example), Assay Type (select, Gene Expression in the example), Provider (Affymetrix in the example), Version Number (1 in the example), Feature Type (in_situ_oligo_features (MO) ni the example) and Organism (Homo sapiens (ncbitax)).
Selecting an array design file
Selecting the Array design file format
Submitting files to upload
Array Design Files, Imported and Importing (Being Validated)
Array Design Files, Imported
After data has been imported into an experiment, the array design associated with that data cannot be removed from the experiment's list of array designs. Conversely, once an array design has been imported, the file associated with it cannot be changed. Array designs that are not associated with an experiment can now be deleted. To delete an array design, follow this step:
Array Design Files with Delete Icon and Confirmation Window
In caArray 2.2, any logged in user can edit an array design. To edit an array design, follow these steps:
Array Design Details Dialog Open for Editing in V2.3 and V2.2 and Under with Fewer Fields Open for Editing
Once an array design has been imported and parsed into caArray, the array design file associated with it cannot be changed. You will have to delete the existing one and upload a new one. This can be done only if there is no experiment data associated with this array design file.
The only array design file that can be replaced is the one imported without validation and parsing. (For more information on the definition of different file types, refer to caArray 016 - Which file can be parsed into caArray? What is the benefit of file parsing? Files Recognized by caArray.)
To replace an array design file, follow these steps:
Replacing an Array Design File
Please leave your comment in the caArray End User Forum.