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Archived Comments for: ProGenExpress: Visualization of quantitative data on prokaryotic genomes

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  1. Purported limitations

    Trinad Chakraborty, Institute of Medical Microbiology

    13 April 2005

    In the background section, the author refers to limitations in the use of GenomeViz to plot quantitative data. In particular, the assertion that quantitative data may only be represented in a color scale is false. This is clearly documented in Figure 3 of the manuscript ( Indeed, GenomeViz provides users with a choice of plotting the data on color scales or choosing a bar-plot representation. Visualization of complex data such as a time course experiment can be achieved by plotting each of the time course measurements in a different genome circle. Thus, it is possible to plot and visualize measurements from up to eight different time points simultaneously.

    The comments regarding GenomeViz are misleading and we feel such arguments will unnecessarily deter other users from experimenting with it.

    Competing interests

    None declared

  2. T Chakraborty - a response

    Mick Watson, Institute for Animal Health

    20 April 2005

    I would first like to apologise for misrepresenting GenomeViz. I must admit to having only used GenomeViz very sparingly as I have had problems installing it. Although it is clear to me now that GenomeViz can plot numerical data as barplots, I still feel that the underlying issue remains - namely that it can be difficult to perform accurate visual comparisons between numerical data points using all of the software I mentioned e.g. the difference between 3.9 and 4.1 may be difficult to see by eye.

    My intention was not to mislead or unnecessarily deter users from trying out GenomeViz, which looks to be a very useful piece of software. The major advantages of ProGenExpress remain it's implementation in R, it's integration with Bioconductor and it's cross-platform compatibility.

    Competing interests

    I am the author of this paper