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how_to:generateamtdb [2012/02/29 11:57] 132.168.73.124 |
how_to:generateamtdb [2012/02/29 12:03] 132.168.73.124 |
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:!: **Requirements** \\ | :!: **Requirements** \\ | ||
Context have to be **[[how_to:proteingrouping|grouped]]** previously. | Context have to be **[[how_to:proteingrouping|grouped]]** previously. | ||
- | You may want apply some filters during this step: | + | You generally apply some filtering during and/or after the protein grouping step to suppress: |
* Reverse proteins | * Reverse proteins | ||
* Species with a sequence < 7 | * Species with a sequence < 7 | ||
* Proteins identified by only 1 species with a score < 60 | * Proteins identified by only 1 species with a score < 60 | ||
- | :!: **Notes** \\ | + | :!: **Note**: **[[how_to:alignretentiontime|Retention time alignment]]** & **[[how_to:recomputeretentiontime|retention time recomputing]]** algorithms may have to be run before creating |
- | **[[how_to:alignretentiontime|Retention time alignment]]** & **[[how_to:recomputeretentiontime|retention time recomputing]]** algorithms may have to be run before creating | + | |
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===== AMT database model ===== | ===== AMT database model ===== | ||
- | + | When creating an AMT database (MS Access) from hEIDI, following tables are populated: | |
- | Below is the actual AMT database model showing relationships between tables in MS Access.\\ | + | |
- | + | ||
- | When exporting an AMT database from hEIDI, 5 tables are populated: | + | |
* **__Table AMT__**: species of the exported User context | * **__Table AMT__**: species of the exported User context | ||
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* delay_minutes: analysis delay in minutes | * delay_minutes: analysis delay in minutes | ||
- | UMCs tables are populated when using '[[how_to:includeumcinamtdb|Read UMCs]]' tool. | + | :!: **Notes**: |
+ | * UMCs tables were populated using '[[how_to:includeumcinamtdb|Read UMCs]]' tool until hEIDI 1.12.0.\\ | ||
+ | * Since hEIDI 1.13.0, UMCs result files are included into MSIdb (instead of AMTdb) | ||
{{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} | {{:how_to:amtexport_relationsmsaccess.png|Relationships in the AMT database (MS Access)}} |