| 1 | Simplified Process for Running Tab2Mage Importer on a new BASE Installation |
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| 2 | ============================================================ |
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| 3 | |
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| 4 | AFFYMETRIX |
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| 5 | -------------------- |
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| 6 | - Install a new base instance |
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| 7 | |
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| 8 | - log in as root and create an administrator account, |
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| 9 | |
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| 10 | - log into base as the administrator, using the newly created account |
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| 11 | |
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| 12 | - go to Administrate -> Plugins -> Definitions |
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| 13 | Click New to create the Affymetrix Array Design Batch Importer Plugin. Follow further instructions on : plugin website if required. |
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| 14 | |
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| 15 | - go to View - > File |
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| 16 | upload zip files containing all the array design for affymetrix experiments |
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| 17 | |
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| 18 | - go to LIMS -> Array Designs -> |
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| 19 | click on the import tab |
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| 20 | on the dialog, select affymetrix array design batch importer and follow the process through to finish |
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| 21 | all the array deisgn are created. |
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| 22 | |
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| 23 | - go to Administrate -> Plugins -> Definitions |
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| 24 | Click New to create, share and configure the Annotation Types and Cv Loader Plugin. |
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| 25 | use the sample comfiguration file on the plugin site(annotationtypecvimporter.xml) to configure the plugin. |
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| 26 | Upload the file into base |
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| 27 | go to Adminstrate -> Plugin Configuration |
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| 28 | Click the Import tab, select "Plugin Configuration Importer" |
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| 29 | click browse to select the uploaded xml file (annotationtypecvimporter.xml), click next and finish |
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| 30 | |
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| 31 | Follow further instructions on : plugin website if required |
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| 32 | |
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| 33 | - go to Administrate -> Plugins -> Definitions |
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| 34 | Click New to create and share the Tab2Mage Importer Plugin. Follow further instructions on : plugin website if required. |
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| 35 | |
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| 36 | - go to View - > File and upload zip files containing all the raw data files and the tab2mage file for the affymetrix experiment |
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| 37 | |
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| 38 | - go to View ->Experiment |
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| 39 | create a new Affymetrix experiment |
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| 40 | on experiment view page click on the import tab and select Tab2Mage Importer |
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| 41 | Run the Tab2Mage Importer, following the instructions on plugin website |
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| 42 | |
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| 43 | |
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| 44 | PRESTO! following the above process should upload the experiment for you. |
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| 45 | |
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| 46 | |
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| 47 | ------------------------------------------------------------------------------------------------------------ |
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| 48 | |
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