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Note
This illustration was presented using *caArray version 2.3.1. Depending on the version you use, the screen layouts may be slightly different, however, the basic design and the steps are similar.
*Before Log into caArray application, please download the sample array design file Hu6800.zip, and the sample experiment data file caArray_golub-00095_files.zip, if you have not already done so. You may unzip the design file to get Hu6800.cdf, but do not extract the sample data file caArray_golub-00095_files.zip.'''

<div align="Left">Step 1: Design File Upload </div>

*Step 1.1. Log into caArray Application. Click on the "MANAGE ARRAY DESIGNS" button under "CURATION" on the right side of the page, see Fig1.1a. A new window "Manage Array Designs" will apear, see Fig1.1b. Before uploading the design file, check if your application already has a copy of the deisgn file by the same name. If yes, skip design file upload, go to [Step 2|https
//cabig-kc.nci.nih.gov/Molecular/KC/index.php/New_Sample_Data_page#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.*
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Image:Fig1.1a.png| Fig. 1.1a Click on the picture to enlarge
Image:Fig1.1c.png| Fig. 1.1b Click on the picture to enlarge
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;Step 1.2. On "Manage Array Designs" page, Click on the "Import a New Array Design" button, see Fig.1.1. Another page "New Array Design (Step 1)" will appear, see Fig. 1.3. Fill out the "New Array Design" form with the information shown in Fig.1.3. Then click on "Next".
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Fig1.2.png| Fig. 1.2 Click on the picture to enlarge
Image:Fig1.3.png| Fig. 1.3 Click on the picture to enlarge
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;Step 1.3. The page "New Array Design(Step 2)" will appear. 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.
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Fig1.4.png| Fig. 1.4 Click on the picture to enlarge
Image:Fig1.5.png| Fig. 1.5 Click on the picture to enlarge
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;Step 1.4. On clicking the "Save" button, the screen shown in Fig 1.6 will apear. Click on "Close window and go to Manage Array Designs". You will be brought back to "Manage Array Designs" screen, as shown in Fig 1.1b. (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.)
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Fig1.6.png| Fig. 1.6 Click on the picture to enlarge
Image:Fig1.1c.png| Fig. 1.1b Click on the picture to enlarge

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<div align="Left">*Step 2

Experiment Data File Upload *</div>

Step 2.1 Click on the "CREATE/PROPOSE EXPERIMENT" button under "EXPERIMENT MANAGEMENT" on the left side menu bar. The "Overall Experiment Characteristics" screen will appear. See Fig 2.2.
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Fig2.1.png| Fig. 2.1 Click on the picture to enlarge
Image:Fig2.2.png| Fig. 2.2 Click on the picture to enlarge
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;'''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 on the "Save" button.
Sample Text:

Title: Diffuse large B-cell lymphoma outcome prediction

Description: Diffuse large B-cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is curable in less than 50% of patients. Prognostic models based on pre-treatment characteristics, such as the International Prognostic Index (IPI), are currently used to predict outcome in DLBCL. However, clinical outcome models identify neither the molecular basis of clinical heterogeneity, nor specific therapeutic targets. We analyzed the expression of 6,817 genes in diagnostic tumor specimens from DLBCL patients who received cyclophosphamide, adriamycin, vincristine and prednisone (CHOP)-based chemotherapy, and applied a supervised learning prediction method to identify cured versus fatal or refractory disease. The algorithm classified two categories of patients with very different five-year overall survival rates (70% versus 12%). The model also effectively delineated patients within specific IPI risk categories who were likely to be cured or to die of their disease. Genes implicated in DLBCL outcome included some that regulate responses to B-cell-receptor signaling, critical serine/threonine phosphorylation pathways and apoptosis. Our data indicate that supervised learning classification techniques can predict outcome in DLBCL and identify rational targets for intervention. **NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897558868337:1'.

;'''Step 2.3. The screen shown in Fig 2.3 will be appear. Check for "Experiment has been successfully saved" message. Click on the "Contacts" tab. Fill the form with your information. You can also edit the contact information from the screen shown in Fig 2.4
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Fig2.3.png| Fig. 2.3 Click on the picture to enlarge
Image:Fig2.4.png| Fig. 2.4 Click on the picture to enlarge
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;Step 2.4. Click on the "Data" tab, then Click on the "Upload New File(s)" button, see Fig 2.5. A new popup window, "Experiment Data Upload" window will appear, see Fig 2.6.
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Fig2.5.png| Fig. 2.5 Click on the picture to enlarge
Image:Fig2.6.png| Fig. 2.6 Click on the picture to enlarge
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;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.
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;*Step 2.6. Wait until the window "Your file upload is complete" is displayed. Click on "OK" (Fig 2.7). Then click on the "Close Window and go to Experiment Data" button as shown in Fig 2.7. *
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Fig2.7.png| Fig. 2.7 Click on the picture to enlarge
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;Step 2.7. On the main window shown below (Fig2.8), make sure the column "STATUS" displayed 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" will appear (Fig2.9). Select the first option "Autocreate annotation sets...", then click on the "Import" button.
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Fig2.8.png| Fig. 2.8 Click on the picture to enlarge
Image:Fig2.9.png| Fig. 2.9 Click on the picture to enlarge
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;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.
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Fig2.10.png| Fig. 2.10 Click on the picture to enlarge
Image:Fig2.11.png| Fig. 2.11 Click on the picture to enlarge
Image:Fig2.12.png| Fig. 2.12 Click on the picture to enlarge
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;'''Step2.9. To make the experiment data public so people other than you can view your data, click on the "My Experiment Workspace" button (Fig2.13). Locate the experiment of interest on "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.
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Fig2.13.png| Fig. 2.13 Click on the picture to enlarge
Image:Fig2.16.png| Fig. 2.14 Click on the picture to enlarge
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'''Step2.10. 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 accessable by the pubic (Fig.2.18).
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Fig2.17.png| Fig. 2.17 Click on the picture to enlarge
Image:Fig2.18.png| Fig. 2.18 Click on the picture to enlarge
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<div align="Left">*Step 3

Verification of Data Sharing on caGrid *</div>
For those Institutions that register their caArray instance on caGrid, the public data is available to other integrated tools that use the caGrid service. To verify whether your caArray data is shared on caGrid, go to CaArray071 and follow the instructions.

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Content

Space Tools

<font size="4" ><div align="Left">Step 1: Design File Upload </div></font>

<font size="4" ><div align="Left">*Step 2

<font size="4" ><div align="Left">*Step 3

Content

Space Tools

A Step-by-Step Guide for Sample Data Loading and Testing

<font size="4" ><div align="Left">*Step 1: Design File Upload *</div></font>

<font size="4" ><div align="Left">*Step 2

<font size="4" ><div align="Left">*Step 3

<font size="4" ><div align="Left">Step 1: Design File Upload </div></font>