Cluster analysis by K-means (analysis)

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Analysis title
Data-Cluster-analysis-by-K-means-icon.png Cluster analysis by K-means
Provider
Institute of Systems Biology
Class
ClusterAnalysis
Plugin
ru.biosoft.analysis (Common methods of data analysis plug-in)

Contents

Goal:

Genes are grouped into clusters so that those in one cluster exhibit maximal similarity, whereas those of different clusters are maximally dissimilar.

Input:

A table of genes or probes with their expression values or fold change calculated. Depending on the algorithm, input of certain parameters is required.

Output:

A table with the same genes grouped into clusters.

Parameters:

  • Experiment data - experimental data for analysis.
    • Table - a table with experimental data stored in repository.
    • Columns - the columns from the table which should be taken for the clustering analysis.
  • Cluster algorithm - the version of the K-means algorithm to be applied [1-4].
  • Cluster number - the number of clusters into which the input data will be divided.
  • Output table - name and path in the repository under which the result table will be saved. If a table with the specified name and path already exists, it will be overwritten.

Further details:

The clustering is done with the K-means algorithm as implemented in the R package (http://www.r-project.org/).

References:

  1. Forgy, E. W. (1965) Cluster analysis of multivariate data: efficiency vs interpretability of classifications. Biometrics 21, 768�769.
  2. Hartigan, J. A. and Wong, M. A. (1979). A K-means clustering algorithm. Applied Statistics 28, 100�108.
  3. Lloyd, S. P. (1957, 1982) Least squares quantization in PCM. Technical Note, Bell Laboratories. Published in 1982 in IEEE Transactions on Information Theory 28, 128�137.
  4. MacQueen, J. (1967) Some methods for classification and analysis of multivariate observations. In Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, eds L. M. Le Cam & J. Neyman, 1, pp. 281�297. Berkeley, CA: University of California Press.
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