1 | | It is the same problem as in #1238. The `SSP_*_SCORE` annotations should be defined as TEXT type. Existing SSP annotations need to be removed, and the SSP plug-in re-executed. |
| 1 | It is the same problem as in #1238. The `SSP_*_SCORE` annotations should be defined as TEXT type. Existing SSP annotations need to be removed, and the SSP plug-in re-executed. |
| 2 | |
| 3 | The update process involves some manual steps: |
| 4 | |
| 5 | 1. Export a file with the ID of all !StringTie raw bioassays that already have one or more SSP annotaions. No other columns are needed. The Excel format can be used. Save to exported file to the local computer. |
| 6 | 2. Add headers to the exported file for all SSP annotation types: |
| 7 | {{{ |
| 8 | SSP_CC15 |
| 9 | SSP_CC15_Scores |
| 10 | SSP_ER |
| 11 | SSP_ER_Scores |
| 12 | SSP_ERBB2 |
| 13 | SSP_ERBB2_ERn |
| 14 | SSP_ERBB2_ERn_Scores |
| 15 | SSP_ERBB2_ERp |
| 16 | SSP_ERBB2_ERp_Scores |
| 17 | SSP_ERBB2_Scores |
| 18 | SSP_IntClust10 |
| 19 | SSP_IntClust10_Scores |
| 20 | SSP_Ki67 |
| 21 | SSP_Ki67_Scores |
| 22 | SSP_NHG |
| 23 | SSP_NHG_Scores |
| 24 | SSP_PAM50subtype |
| 25 | SSP_PAM50subtype_Scores |
| 26 | SSP_PR |
| 27 | SSP_PR_Scores |
| 28 | SSP_RORasT0 |
| 29 | SSP_RORasT0_Scores |
| 30 | SSP_Subtype |
| 31 | SSP_Subtype_Scores |
| 32 | }}} |
| 33 | Use the attachment:headers-for-import.txt file as template. |
| 34 | |
| 35 | 3. Upload the file to BASE and run the **Annotation importer** plug-in. Make sure that **Identification method=Internal ID**, that all columns are mapped correctly and that the **Remove existing** option is enabled in the third step. |
| 36 | 4. When all annotations have been deleted it should be possible to delete all SSP_* annotation types as well. Do not forget to empty the trashcan. |
| 37 | 5. Update Reggie and run the **Installation wizard**. The SSP annotation types should be re-created. |
| 38 | 6. All existing !StringTie raw bioassays need to be re-analyzed by the SSP plug-in. |