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Table 2 Algorithm of clusters search

From: A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

Clusters_search(γ):

 

   1. Clique and pseudoclique search:

• Find the maximal cliques and remove the cliques of size two if their nodes have more than 1 neighbour

 

• For all cliques C, remove the nodes n for which max w(n, i)iCτ(C)

 

• For all cliques C, add to C the γ-dense nodes n such that min w(n, i)iCτ(C)

 

• Remove from the list of cluster the included clusters.

   2. Select clusters according to their s-value:

• Remove the "worst clusters": For all clusters C1, C2 such that | V c 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2FAD@ | ≥ | V c 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIYaGmaeqaaaWcbeaaaaa@2FAF@ |, if | V c 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2FAD@ V c 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIYaGmaeqaaaWcbeaaaaa@2FAF@ | ≥ γ × | V c 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2FAD@ | and s(C1) ≥ s(C2) and Gelnb(C1) ≥ Gelnb(C2) then remove C2.

 

• For all clusters C1, C2 such that | V c 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2FAD@ V c 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIYaGmaeqaaaWcbeaaaaa@2FAF@ | ≥ γ × min(| V c 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2FAD@ |, | V c 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOvay1aaSbaaSqaaiabdogaJnaaBaaameaacqaIYaGmaeqaaaWcbeaaaaa@2FAF@ |), add the nodes of min(s(C1), s(C2)) which have a maximal weight greater than τ(C min ) in max(s(C1), s(C2)).

   3. Select nodes which belong to several clusters:

• For all nodes n which belong to several clusters, remove n from all clusters where it does not have its maximal MeanW.