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Topic: caArray Usage
Release: Up to caArray 2.X
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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 for more details, see caArray010 Where are the Array Design Files for caArray?), many array design files are now available to download at the NCI 's public caArray server, a new feature made available in caArray version 2.3.
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After login to caArray, the option to manage array design will be available in the Curation section at the left menu (circle in red, Figure 1). To select a file to download, following steps below:
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1. Click on "Manage Array Design" at the left menu section (Arrow 1).
*2. * All the design files that have been imported into caArray will be displayed in the main data area (Arrow 2)
*3. * Locate the array design file interested, select "Download" (Arrow 3) to launch the download.
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Upload a new array design fileAny 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, user can initiate the file upload into caArray: |
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*1. * Click on *Import a New Array Design *(Arrow 4 in Figure 1).
2. * This opens the *New Array Design dialog box (Figure 2).
3. * Enter the appropriate information in the fields provided on *Array Design Details form.
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*4. * Click on "Next" to select an array design file interested.(Figure 3).
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*5. * Identify the array design file format in the drop-down list (Figure 4).
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*6. * Multiple array design Files can be submitted to upload at the same time. Click on "Add More Files" to select a new file. After all of the files selected, submit the files to upload by clicking on "Save" (arrow in Figure 5).
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Validate an array design file |
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*1. * Upon the array design file is uploaded, caArray will automatically initiate the validation process (shown as "Importing" in Figure 5). If the file is from a supported array provider, caArray will mark the file as "Imported" after the validation (Figure 6).
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*2. * For more information on the different states of the array design files, refer to caArray Status of Importing: Imported vs Imported Not Parsed
Delete, Edit and Replace an array design file in caArrayDelete an Array DesignAfter 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:
Edit an Array DesignIn caArray 2.2, any logged in user can edit an array design. To edit an array design, follow these steps: 1. On the row corresponding to the array design, click the Edit icon (Figure 8).
2. The required fields become editable; enter any edits.
Replace an Array DesignOnce 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 Which File Can Be Parsed into caArray?). To replace an array design file, follow these steps: |
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*1. * Find the file that is replaceable (the file with a status of "Imported (Not Parsed)" (circle in red in Figure 10).
*2. * Click on "Edit File" icon (Arrow) to activate "Upload Array Design File" Window.
*3. * Browse and find the new array design file.
*4. * Save the new file by clicking the Save button.
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Have a comment? Please leave your comment in [ caArray End User Forum|http://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=436]
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