Description Usage Arguments Details Value Note Author(s) References Examples

This function performs repeated soft clustering for a range of cluster numbers c and reports the number of empty clusters detected.

1 | ```
cselection(eset,m,crange=seq(4,32,4),repeats=5,visu=TRUE,...)
``` |

`eset` |
object of class |

`m` |
value of fuzzy c-means parameter |

`crange` |
range of number of clusters |

`repeats` |
number of repeated clusterings. |

`visu` |
If |

`...` |
additional arguments for underlying |

A soft cluster is considered as empty, if none of the genes has a corresponding membership value larger than 0.5

A matrix with the number of empty clusters detected is generated.

The `cselection`

function may help to determine an accurate cluster number. However, it should be used with care, as the determination remains difficult especially for short time series and overlapping clusters. A better way is likely to perform clustering with a range of cluster numbers and subsequently assess their biological relevance e.g. by GO analyses.

Matthias E. Futschik (http://www.cbme.ualg.pt/mfutschik_cbme.html)

M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, 3 (4), 965-988, 2005

L. Kumar and M. Futschik, Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2(1) 5-7,2007

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)
#### parameter selection
# Empty clusters should not appear
cl <- mfuzz(yeastF,c=20,m=1.25)
mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))
# Note: The following calculation might take some time
tmp <- cselection(yeastF,m=1.25,crange=seq(5,40,5),repeats=5,visu=TRUE)
# derivation of number of non-empty clusters (crosses) from diagnonal
# line indicate appearance of empty clusters
# Empty clusters might appear
cl <- mfuzz(yeastF,c=40,m=1.25)
mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))
}
``` |

Mfuzz documentation built on Nov. 1, 2018, 5:03 a.m.

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