To show how to use Cromwell, one of our current analysis packages, we've created an example using serum quality control (QC) data derived from the Pusztai et al 2004 low-mass March03 dataset. This example is not completely self-contained. It requires MATLAB and the Rice Wavelet Toolbox. The latter can be downloaded from www-dsp.rice.edu/software/rwt.shtml. The Cromwell package is decribed in Coombes et al, Proteomics 2005; to appear.
At this point, the MATLAB scripts we have provided work on text files containing only the sample data from the XML files. We have provided a simple Perl script, xml2txt.pl, to strip the required data from the XML files. Both the Perl script and the processing scripts assume a fairly specific directory structure, so hardcoded names must be changed for adaptations.
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