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Question: Where are the Array Design Files for caArray?
Topic: caArray Usage
Release: Up to caArray 2.X
Date entered: 02/20/2009
Answer
New Feature in caArray 2.3 and Up
Starting in caArray 2.3 and up, users can download any array design file stored NCI's public caArray instance. Simply locate the array design file of interest in caArray and launch the download process.
Finding Array Design Files
No array design information is present with a new caArray installation. This feature provides the flexibility for an organization to upload only the designs they use. This reduces the overhead introduced by loading unnecessary designs, which are often of significant size (100's of megabytes or more). This does mean, however, that users must find and upload all the necessary array design files into their caArray server. Searching for the array design files could be confusing and time consuming.
It is possible, if you are not using a new instance of caArray, that the array design file you need already exists in caArray. For example, many array design files have been uploaded into NCI's caArray by the users, and they can be reused for other experiments on the same server. The array design files, unlike other array data files however, are not portable in caArray. That is, they cannot be downloaded from one caArray instance and uploaded to a different caArray instance.
The purpose of this knowledge base entry is to consolidate information in one convenient place about the location of array design files from different vendors. The list below is not yet complete. Contributions from the caArray user community are highly appreciated. Please post any links or suggestions in the caArray End User Forum.
Array Design Files
Array Provider | Array Design File | Comments | File Location | Supported by caArray? |
|---|---|---|---|---|
Affymetrix | .CDF, .PGF, .CLF | Free Registration is required to download array design .Zip file. After downloading the selected package, one needs to drill down to find the folder containing the .CDF file. | Yes, Parsed | |
GenePix | .GAL | The GenePix array design file needs to be created by the user. The link provided the details of the GenePix array design file format, as well as the instructions to create one. | Yes, Parsed | |
Illumina | .CSV | Illumina's arrays are whole-genome arrays. the BGX version of the array design files for Illumina is yet to be supported by caArray. Please use the text version instead. | Yes / Parsed | |
Agilent | .CSV/.XML, .GAL | The array design file can be pulled out from Agilent's website based the barcode on the array chip. For example, barcode 251643612131 is on the array chip for one of your experiment. You can submit the barcode 251643612131 in the "Array Barcode Submission Form" (the 2nd link on the right), which will then return the array design file for Human miRNA Microarray (G4470A). Agilient also provides array design files in .GAL format, which are created with GenePix's scanner service. To upload these Agilent's .GAL files, please select GenePix's .GAL as the uploading template. | No, Imported but Not Parsed | |
ImaGene | .TPL | N/A, Contribution Appreciated. | No, Uploaded but Not Parsed | |
Nimblegen (Roche) | .NDF | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
ScanArray | – | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
UCSF Spot | .SPT | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
MAGE-TAB | .ADF | Need to create | No, Uploaded but Not Parsed |
Good to Know
Before you submit your new array design file for uploading, make sure that you have selected the correct file format from File Format drop down list. The default selection of 'Automatic' from File Format might fail in recognizing some file types.
Further Readings on Uploading Array Design Files into caArray
- Importing an Array Design into caArray
- Import Array Designs Use Case Specification
- Check Existing Array Design Files on caArray
- Managing Array Designs
Useful Tools
Spotter file to ADF Converter. This converter tool can convert .GAL design file for Biorobotics, Genetix, Agilent, Clontech, Virtek to MAGE-TAB formatted Array Design File (ADF).
Historical link http://www.ebi.ac.uk/cgi-bin/microarray/gal2adf2mart.pl
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