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caArray Usage

Date entered: 02/20/2009

Release Up to: caArray 2.X

Question: Where Are the Array Design Files for caArray?

caArray Usage

Date entered: 02/17/2009

Release Up to: caArray 2.2

Question: *A Checklist: Building caArray's MAGE-TAB Annotation Files *

Answer:

New Feature in caArray 2.3 & Up

Starting in caArray 2.3 & Up, users may download any array design file stored NCI's public caArray instance. Simply locate the array design file interested in caArray and launch the download process.

Find the Array Design Files

caArray allows the users to upload array design information on an as-needed basis. Therefore, No array design information is present with a new caArray installation. While this feature provides the flexibility for an organization to upload only the designs they use (and as a result reduce the overhead introduced by loading unnecessary designs - which are often of significant size (100's of megabytes or more)), it also means that the users have to 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.

Many array design files have been uploaded into NCI's caArray by the users, they can be reused for other experiments on the same server. The array design files, unlike other array data files, are not portable in caArray. For example, they can not be downloaded from one caArray instance and uploaded to a different caArray instance. The purpose of this knowledge base entry is to consolidate information on the whereabouts of array design files from different providers in one convenient place. The list below is not yet complete. Contributions from the caArray user community are highly appreciated. Please post any links or suggestions in caArray End User Forum.

Table 1. 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.

  • Affymetrix Design Library | 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.

  • GAL Format
  • Making GAL Files | 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.

  • Whole Genome Design Files | 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. |

N/A, Contribution Appreciated. | Imagene User Guide | 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 | More on MAGE-TAB Files | No, Uploaded but Not Parsed |

Good to Know: Before you submit your new array design file for uploading, please 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

  1. Import Array Designs Use Case Specification
  2. Check Existing Array Design Files on caArray

Useful Tools

  1. 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).

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