 |
Page History
...
| Panel | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| |||||||||
|
| Tip | ||
|---|---|---|
| ||
Depending on the version you use, the screen layouts may be slightly different, however, the basic design and the steps are similar. |
...
Log into the caArray Application. Click on the "MANAGE ARRAY DESIGNS" button under "CURATION" on the right left side of the Welcome page.
A new windowpage, "Manage Array Designs", opens. Before uploading the design file, check if your application already has a copy of the design file by the same name. If yes, skip the design file upload and proceed to #Step 2 Experiment Data File Upload. You can use this design file for your experiment. If not, follow Step 1.2 to upload a new design file.
caArray Data Portal Welcome Page
Manage Array Designs Page - 1
- 1b
Steps 1.2
On the "Manage Array Designs" page, Click click the "Import a New Array Design" button, see Fig. 1.1. Another page, "New Array Design (Step 1)", opens, see Fig. 1.3. Fill out the "New Array Design" form with the information shown in Fig.1.3Description (Affymetrix Hu6800 Sample Arrya Design in the example); Selected Assay Type (Gene Expression is selected in the example); Provider (here Affymetrix); Version number (here 1.0); Feature Type (in_situ_oligo_features (MO) in the example); and Organism (Homo sapiens (ncbitax) in the example). Then click "Next".
*Manage Array Designs Page with Import a New Array Design Button"
New Array Design (Step 1) Page with Form Completed - 2
- 3
Step 1.3
The page "New Array Design (Step 2)" opens. Click the "Browse" button. Browse to the location where the sample array design file (Hu6800.cdf) was unzipped. Then click "Save". See Fig 1.4 and Fig 1.5.
New Array Design (Step 2) Page with Browse Button
New Array Design (Step 2) Page with Save Button
- 4
! - 5
Step 1.4
On clicking the "Save" button, the screen shown in Fig 1.6 opens. Click "Close window and go to Manage Array Designs". The "Manage Array Designs" re-opens, as shown in Fig 1.1b (c). (Please note that for large array design files, the importing process might take a while. An array design can only be used when it is fully imported.)
- 6
- 1b
Step 2 Experiment Data File Upload
...
Click the "CREATE/PROPOSE EXPERIMENT" button under "EXPERIMENT MANAGEMENT" on the left side menu bar. The "Overall Experiment Characteristics" screen opens. See Fig 2.2.
- 1
- 2
Step 2.2
Fill out the form with the information shown in Fig 2.2. You can use your own description or use the sample text displayed below. Make sure "Array Designs" field is selected with the right platform (highlighted in blue). Click the "Save" button.
...
The screen shown in Fig 2.3 opens. Check for the "Experiment has been successfully saved" message. Click the "Contacts" tab. Fill the form with your information. You can also edit the contact information from the screen shown in Fig 2.4.
Step 2.4
Click the "Data" tab. Then Click the "Upload New File(s)" button, see Fig 2.5. A new popup window, "Experiment Data Upload" window opens, see Fig 2.6.
- 5
- 6
Step 2.5
Browse to the location where the sample experiment Data file (caArray_golub-00095_files.zip) was saved and click on the "Upload" button, see Fig 2.6.
...
Wait until the window "Your file upload is complete" is displayed. Click "OK" (Fig 2.7). Then click the "Close Window and go to Experiment Data" button as shown in Fig 2.7.
- 7
Step 2.7
On the main window shown below (Fig2.8), make sure the column "STATUS" displays the word "Uploaded" for each file. Select the check boxes for all experiment data sets and then click on "Import" button. A new window "Import Options" opens (Fig2.9). Select the first option "Autocreate annotation sets...", then click on the "Import" button.
- 8
Step 2.8
Depending on the speed of the machine and the size of the data, it may take a few minutes for the sample data to be imported. Check the status of the import by Clicking on the "Refresh Status" button (Fig2.10). The initial status will be shown as "In queue" (Fig2.10). When the import is complete, no data will be displayed under the "Manage Data" tab (Fig2.11). Click on the "Imported Data" tab to view imported data file (Fig2.12). If you completed all these steps, Congratulations! You have just successfully created an experiment and deposited your microarray experiment data into the caArray.
Step 2.9
To make the experiment data public so people other than you can view your data, click the "My Experiment Workspace" button (Fig2.13). Locate the experiment of interest on the "My experiment Workspace" page. Click on the "Permissions" icon (Fig2.13), the "Experiment Permissions" page will appear (Fig2.14). Click on the "Edit Access Control" button in the left panel.
Step 2.10
In the new window appeared, select "Read" from the drop down list in the right panel, then click on the "Save" button (Fig 2.17). Your experiment is now set to be accessible by the pubic (Fig.2.18).
Step 3 Verification of Data Sharing on caGrid
...
