userguide:proteinfiltering
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userguide:proteinfiltering [2010/04/14 11:23] 132.168.73.247 |
userguide:proteinfiltering [2010/11/05 11:06] 132.168.74.230 |
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| - | ====== Filter proteins or protein groups ====== | + | ====== How-to filter proteins or protein groups ====== |
| - | On a [[userguide:contextdefinition| User Context]] it is possible to apply filters. Filter will mark as //hidden// (or //masked//) protein groups or proteins inside protein groups (depending on user choice) which respect user defined criteria. | + | On a [[userguide:contextdefinition| User Context]] it is possible to apply filters. Filter will mark as //hidden// (or //masked//) protein groups or proteins inside protein groups (depending on user choice) according user defined criteria. |
| - | * If protein groups are filtered, the typical protein is considered but the whole group is (eventually) marked as //hidden//. | + | * If protein groups are filtered (i.e. "Apply to proteins" is NOT checked), the typical protein is considered but the whole group is (eventually) marked as //hidden//. |
| - | * If proteins are filtered, each proteins of each protein groups are considered and (eventually) marked as //hidden//. If typical protein is set //hidden//, then another sameset protein is set as typical. If there is no more none //hidden// sameset then the whole protein group is set as //hidden//. | + | * If proteins are filtered (i.e. "Apply to proteins" is checked), each protein from every protein groups are considered and (eventually) marked as //hidden//. If a typical protein is //hidden//, then another sameset protein become the typical protein. If there is no more //visible// sameset protein then the whole protein group is set as //hidden//. |
| The available filters are described in the how to [[how_to:proteinfiltering|filter proteins [groups] ]]. | The available filters are described in the how to [[how_to:proteinfiltering|filter proteins [groups] ]]. | ||
| ===== Impact of masking proteins [groups] in algorithms ===== | ===== Impact of masking proteins [groups] in algorithms ===== | ||
| - | Once protein or proteins groups are marked as masked, they will be taken into account is some operations. | + | Once a protein or a protein groups is masked, it will be taken into account is some operations. |
| ==== Masked protein groups ==== | ==== Masked protein groups ==== | ||
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| The export operations (for AMT or reports) will only export valid (none masked) protein groups. This is also the case for ''Contexts comparison'' algorithm. | The export operations (for AMT or reports) will only export valid (none masked) protein groups. This is also the case for ''Contexts comparison'' algorithm. | ||
| - | The other algorithms (change master / spectral count / protein grouping (peptide to consider) are not be impacted and (even if not necessary), they could be applied to all protein groups. | ||
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| + | __**The other algorithms (change master / spectral count / protein grouping (peptide to consider) are not impacted and (even if not necessary), they could be applied to all protein groups.**__ | ||
| + | ==== Masked proteins==== | ||
| - | ==== Hidden protein ==== | + | If user choose to apply filter on individual proteins, valid protein groups may contains valid and masked proteins. |
| - | Hidden individual protein have more impact as in a //valid// protein group, only some of the proteins may be //valid//. | + | In visualization, the [[userguide:proteingroups|protein group view]] identify //masked// proteins in sameset and/or subset lists. |
| - | In visualization, the protein group view //hidden// proteins are identified. | + | For the export : |
| - | The export also have to considerate only none hidden proteins when exporting protein groups details or AMT db. | + | * only valid (none masked) protein are considered when exporting to AMT db. |
| - | The contexts comparison algorithm is impacted in the same way as when protein groups are masked : only valid protein should be considered. In the same way, change typical protein does not select //hidden// protein as typical ! | + | * for reports, only one report is impacted (same subset detail report) and for each protein in valid protein groups, the masked property is indicated. |
| - | The other algorothms (spectral count / grouping (peptide to consider) should not be impacted). | + | |
| - | ===== Hidden proteins group in browser ===== | + | * The ''Contexts comparison'' algorithm is impacted in the same way as when protein groups are masked : only valid proteins should be considered. |
| + | * ''Change typical protein'' operation does not select //masked// protein as typical ! | ||
| - | ===== Hidden proteins in protein groups ===== | + | __**The other algorithms (spectral count / grouping (peptide to consider) are not impacted.**__ |
userguide/proteinfiltering.txt · Last modified: 2010/11/05 11:08 by 132.168.74.230
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