Biomedical Engineering Reference
In-Depth Information
hand side). Some, but not complete, separation in the two plant genotypes
is seen. A new model containing just the plant samples would be the
logical next step in the analysis. Figure 4.16(c) shows the loadings plot,
which shows the pattern of the metabolites corresponding to the patterns
observed in the scores plot. It appears that glutamine, gaba and citric acid
are higher for the WT fruits, and glutamic acid is higher in the controls.
Figure 4.16(d) shows the model is predictively sound as both the variance
explained (R2) and predictive variance(Q2) are high.
Further possibilities for analysis may entail the use of the pls
package for PLS-DA replacing the Y variable with class membership
(0 or 1) for the genotypes or the more sophisticated kopls. This exercise
is left for the reader to complete using the general principles outlined
above.
4.9 Other open source packages
There are many more useful packages being developed for mass
spectrometry and 'omics data processing. For example, TOPPView is a
viewer from the OpenMS proteomics pipeline for the analysis of HPLC/
MS data [48]. A full tutorial is available [49]. Cytoscape [50, 51] is an
open source platform for network visualisation with good connectivity to
bioinformatics resources. Network features such as node and edge
parameters may be visualised in many ways, for instance levels of detected
metabolites may be superimposed on a biological network. There is also
an easy to follow tutorial available [52]. Ondex [53] is another data
integration platform, which is designed to integrate diverse data sets and
has a number of graph visualisation methods.
Finally, no discussion of metabolomics and mass spectrometry would
be complete without mentioning the vast amount of data that studies are
capable of producing. Although original data are often stored in
instruments or dedicated LIMS systems, data modelling produces many
types of intermediate data fi les. Many laboratories are resorting to
backing up data onto high-capacity USB drives for storage or transfer.
Although Linux users are in the fortunate position of having good
operating system support for backups, Cobain Backup 8 [54] is an
excellent open source program for automating backup of data in
Windows. It is able to run either as a background service or an application
and can schedule backup jobs to be started at daily or weekly intervals.
The software supports FTP transfers and contains several methods of
compression and strong encryption.
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