userguide:contextdefinition
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userguide:contextdefinition [2009/12/16 09:09] 132.168.74.230 créée |
userguide:contextdefinition [2010/01/05 12:11] (current) 132.168.74.230 |
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| - | ====== Context comparisons ====== | + | ====== Context ====== |
| ===== Definition ===== | ===== Definition ===== | ||
| - | The purpose is to search for similar [[proteingroups#protein groups]], i.e. protein groups: | + | Context is a central notion in hEIDI. Basically, it contains identification results, i.e. a set of proteins identified by a set of peptides.\\ |
| - | * having the same set of proteins | + | There are two types of contexts in hEIDI: |
| - | * identified by a same set of peptides | + | * Search context: each identification result from Mascot, or from any other identification engine, is automatically "encapsulated" into one Search context. |
| + | * User context: it is created by the user in order to gather together several identification results into a User context. In order to have non-redundant sets of proteins for a given context, proteins need to be grouped to build "Protein Groups". | ||
| - | The Dice coefficient is used to measure similarity (result ranges from 0 to 1). | + | ===== Context tree view ===== |
| + | ==== User Context ==== | ||
| + | {{:usercontextshierarchy.png |}} | ||
| + | A User context is represented by {{:usercontext.png|}}.\\ | ||
| + | A User context contains either child contexts or identifications but can't have both at the same level.\\ | ||
| - | {{:diceCoef.png?102x50}} | + | There are multiple reasons for grouping several identifcations under the same User context: |
| + | * Same biological origin | ||
| + | * Same gel | ||
| + | * Same culture condition | ||
| + | * Same chromatographic column | ||
| + | * ... | ||
| - | ==== Compare two contexts with each other ==== | + | ==== Search Context ==== |
| + | {{:searchcontextshierarchy.png |}} | ||
| + | Search context is represented by {{:context.png|}}. | ||
| - | {{:contextComparison.png?260 }} | ||
| - | It compares every protein groups of the first context with every protein groups of the second context.\\ | ||
| - | Comparing two protein groups each other means: | ||
| - | * Checking the similarity of their protein sets (FIXME sameset and subset) | ||
| - | * Checking the similarity of their peptide sets | ||
| - | * Checking if "master" proteins are identical | ||
| - | ==== Compare N contexts ==== | ||
| - | This comparison is similar to the previous one: similarity measure and FIXME "best alignment"\\ | ||
| - | Each context is compared with a "unique reference". First of all, this reference is built from the identification union, i.e. the parent context. | ||
| - | |{{:contextcomparisonn_1.png?280x235}} | {{:contextcomparisonn_2.png?280x235}} | {{:contextcomparisonn_3.png?280x235}} | | ||
| - | ===== GUI: Compare contexts each other ===== | ||
| - | {{:compareeachother.png |Compare contexts each other}} | ||
| - | - Select the two contexts (for which protein grouping has been executed) you want to compare each other | ||
| - | - Right-click and select "Algorithms->Compare with->Each Other" | ||
| - | - The comparison window display the result | ||
| - | - You can save results as a .xls, .pdf or .html file using the "Export" button | ||
| - | |||
| - | {{:compareeachotherresultwindow.png|Comparison window (Each other)}} | ||
| - | |||
| - | |||
| - | ===== GUI: Compare context with its children ===== | ||
| - | |||
| - | {{:comparewithchildren.png |Compare a context with its children}} | ||
| - | - Select the context of your choice (first, protein grouping needs to be run for this context and its childs) | ||
| - | - Right-click and select “Algorithms→Compare with→Children” | ||
| - | - The comparison window display the result | ||
| - | - Select the characteristic you want to compare | ||
| - | {{:comparechildrenresultwindow.png|Result window when comparing context with its children}} | ||
userguide/contextdefinition.1260950987.txt.gz · Last modified: 2009/12/16 09:09 by 132.168.74.230
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