An R package for NMR Local Intensity Difference Analysis
Nuclear magnetic resonance (NMR) spectroscopy is a measurement technique that utilises the magnetic properties of the atomic nuclei. NMR technology has became famous for its robustness and repeatability for assessing the amount of chemical compounds in various types of biomedical samples.
Locida is an R software package and a Web tool for quick and illustrative group-wise comparisons of 1-D NMR spectral measurements. The mathematical method, local intensity difference analysis, is also called Locida, since the differences in signals are found by inspecting the original (binned) spectral measurements. The method seeks diffences between groups of samples, and illustrates them on a graphical display showing also the original data for each individual sample.
The R package suitable for Linux is Locida_1.0.tar.gz. Windows users should choose Locida_1.0.zip.
Figure.
An example Locida output comparing 1-D NMR spectrum measurements from treated
Nicotiana Tabacum plant samples agains two different (but indistinguishable) control
groups. (Click the image to enlarge it.)
The method was originally developed by A Virkki, H Maaheimo and colleagues at VTT Technical Research Centre of Finland to study the differences between different plant cultures in EU 7th Framework Research Programme SmartCell. The description of the method will be published in due course of that project, whereas interested users can already download the Locida R Package for R command-line analyses, or set up their own Web-based installation by downloading the Locida UI Java Package by cloning the Locida project, and setting up the needed RVaadin run-time environment to launch it. Locida Web interface is implemented in Java by using the Vaadin Web framework, and the inteface communicates with the R language through the RVaadin library. Both the R package and the Web interface are free software and published under GPL v2.