Graphical user interface for Mfuzz package
Mfuzzgui provides a graphical user interface for
clustering of microarray data and visualisation of results.
It is based on the functions of the Mfuzz package.
Mfuzzgui launches a graphical user interface for the Mfuzz package.
It is based on Tk widgets using the R TclTk interface by Peter Dalgaard. It also employs
some pre-made widgets from the tkWidgets Bioconductor-package by Jianhua Zhang for
the selection of objects/files to be loaded.
Mfuzzgui provides a convenient interface to most functions of the Mfuzz package without restriction
of flexibility. An exception is the batch processes such as
cselection routines which
are used for parameter selection in fuzzy c-means clustering of microarray data. These routines are
not included in Mfuzzgui. To select various parameters, the underlying Mfuzz routines may be applied.
Usage of Mfuzzgui does not require assumes an pre-built
but can be used with tab-delimited text files containing the gene expression data.
Note, however, that the clustering is based on the
the ordering of samples (arrays) as
of the columns in the expression matrix of the
exprSet object or in the uploaded table, respectively.
Also, replicated arrays in the
expression matrix (or table) are treated as independent by the
and, thus, should be averagered prior to clustering.
For a overview of the functionality of Mfuzzgui, please refer to the package vignette. For a description
of the underlying functions, please refer to the
Mfuzzgui returns a tclObj object.
The newest versions of
Mfuzzgui can be found at the Mfuzz webpage
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)and Lokesh Kumar
M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-988, 2005.
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW, A genome-wide transcriptional analysis of the mitotic cell cycle, Mol Cell,(2):65-73, 1998.
Mfuzz web-page: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz