NAME

cluster3 — Eisen-clustering of microarray data

SYNOPSIS

cluster3 [-f filename] [-l 0|1] [-u jobname] [-g [0..9]] [-e [0..9]] [-m [msca]] [-k number] [-s 0|1] [-x number] [-y number]

OPTIONS

-h--help

Show summary of options.

-f filename

file loding

-u jobname

Allows you to specify a different name for the output files (default is derived from the input file name)

-l 0|1

Specifies whether to log-transform the data (default is 0, no log-transform)

-k number

Specifies whether to run k-means clustering instead of hierarchical clustering, and the number of clusters k to use (default: 0)

-x number

Specifies the horizontal dimension of the SOM grid (default: 2)

-y number

Specifies the vertical dimension of the SOM grid (default: 1)

-s 0|1

Specifies whether to calculate an SOM instead of hierarchical clustering (default: 0)

-v --version

Show version of program.

-g [0..9] Specifies the distance measure for gene clustering 0: No gene clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 1)

-e [0..9] Specifies the distance measure for microarray clustering 0: No clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 0)

-m [msca] Specifies which hierarchical clustering method to use m: Pairwise complete-linkage s: Pairwise single-linkage c: Pairwise centroid-linkage a: Pairwise average-linkage (default: m)

SEE ALSO

mapletree (1), smile (1).

AUTHOR

This manual page was written by Steffen Moeller moeller@pzr.uni-rostock.de for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.