userguide:contextcomparisons
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userguide:contextcomparisons [2011/02/01 14:41] 132.168.74.230 |
userguide:contextcomparisons [2011/02/01 15:00] 132.168.74.230 |
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| ===== Compare several contexts to their union ===== | ===== Compare several contexts to their union ===== | ||
| - | The purpose is to select contexts to compare, then to compare them to their union, i.e. a parent context, which contains selected children contexts, and for which peptide/protein grouping has been executed.\\ | + | Main steps realized in the comparison process: |
| + | - Retrieve selected contexts to compare | ||
| + | - Know if they are all the children of an existing parent context. If not, create a virtual union parent context (see details in following section) that groups selected contexts and run peptide/protein grouping | ||
| + | - Compare selected contexts to their union (virtual or existing parent) | ||
| ==== Is there a need to create a "virtual" union parent context ? ==== | ==== Is there a need to create a "virtual" union parent context ? ==== | ||
| - | There are 2 possibilities, either the parent union already exists or the parent union needs to be created.\\ | + | There are 2 situations, either the parent union already exists or the parent union needs to be created. In the image below: |
| - | In the image below: | + | * A *virtual* union parent context must be created in **case 1** (the virtual context has no persistence in MSI database, it is only created in-memory for the process) |
| - | * the union parent must be created in **case 1**: it is called //**virtual**// as it is only created in-memory for the process | + | * The union parent context already exists in **case 2** |
| - | * the union parent already exists in **case 2** | + | |
| {{:userguide:comparevirtualconcept_1.png|}} | {{:userguide:comparevirtualconcept_1.png|}} | ||
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| - | {{:groupingsamesetsubset.png |How to obtain a low Protein similarity but with a high Peptide similarity}} Protein group properties: | + | {{:groupingsamesetsubset.png |How to obtain a low Protein similarity but with a high Peptide similarity}} __**Protein group properties**__: |
| * "ProtSim": similarity on the **samesets of proteins** of the two protein groups\\ | * "ProtSim": similarity on the **samesets of proteins** of the two protein groups\\ | ||
| * "AllProtSim": similarity on the **samesets and subsets of proteins** of the two protein groups\\ | * "AllProtSim": similarity on the **samesets and subsets of proteins** of the two protein groups\\ | ||
| * "PepSim": similarity on **peptides** of the two protein groups | * "PepSim": similarity on **peptides** of the two protein groups | ||
| - | * "isSameTypical": indicates if the typical protein is the same between the two protein groups | + | * "isSameTypical": indicates if the **typical protein is the same** between the two protein groups |
| - | * "Typical": the accession of the master protein group | + | * "Typical": the **accession of the master** protein group |
| - | * "Score": score for the protein group | + | * "Score": **score** for the protein group |
| - | * "#Pep": number of peptides for the protein group | + | * "#Pep": **number of peptides** for the protein group |
| - | * "#AllProt": number of proteins in the protein group. 'X(Y,Z)' means a total of X proteins for the whole protein group (X=Y+Z) with Y sameset proteins and Z subset proteins | + | * "#AllProt": **number of proteins** in the protein group. 'X(Y,Z)' means a total of X proteins for the whole protein group (X=Y+Z) with Y sameset proteins and Z subset proteins |
| - | * If Spectral Count algorithm is run previously, Spectral Count values will be available as well | + | * If Spectral Count algorithm is run previously, **Spectral Count values** will be available as well |
| When comparing two protein groups using "Protein" and "Peptide" similarity criteria, you can get four main situations: | When comparing two protein groups using "Protein" and "Peptide" similarity criteria, you can get four main situations: | ||
userguide/contextcomparisons.txt · Last modified: 2012/02/28 11:18 by 132.168.73.124
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