Bioinformatics Advance Access published online on August 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth449
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Division of Genetics and Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, 3050, Australia
* To whom correspondence should be addressed. E-mail: wettenhall{at}wehi.edu.au.
Summary: limmaGUI is a Graphical User Interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of differential expression in complex experiments. limmaGUI provides an interface to the statistical methods of the limma package for R, and is itself implemented as an R package. The software provides point and click access to a range of methods for background correction, graphical display, normalization, and analysis of microarray data. Arbitrarily complex microarray experiments involving multiple RNA sources can be accomodated using linear models and contrasts. Empirical Bayes shrinkage of the gene-wise residual variances is provided to ensure stable results even when the number of arrays is small. Integrated support is provided for quantitative spot quality weights, control spots, within-array replicate spots and multiple testing. limmaGUI is available for most platforms on the which R runs including Windows, Mac and most flavours of Unix. Availability: http://bioinf.wehi.edu.au/limmaGUI.
Revised July 2, 2004
Accepted July 16, 2004
Applications note
limmaGUI: a graphical user interface for linear modeling of microarray data
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