Metabolomics data on spiked apples

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Description

A dataset of LC-MS features, obtained from twenty apples. The last ten apples are spiked with known compounds. This set provides a test case for biomarker selection methods: the task is to retrive the true biomarker variables. The raw LC-MS data hava been converted to CDF format and processed with XCMS to obtain the basepeaks.

Usage

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data(Apples)

Value

The format is a list of four elements:

mz

the m/z values of the features (rounded)

rt

the retention times of the features

apples.data

a matrix containing the intensities in the individual samples

apples.data.vsn

a matrix containing the intesities after variance stabilization and normalization performed with the vsn package

Biom

the indices of the "true" biomarkers

apples.cl

numeric vector encoding which samples are part of the spiked class (code 1) and which ones are controls (code 0)

Author(s)

Francesco Del Carratore

References

P. Franceschi, D. Masuero, U. Vrhovsek, F. Mattivi and R. Wehrens: A benchmark spike-in data set for biomarker identification in metabolomics. J. Chemom. 26, 16-24 (2012)

R. Wehrens, P. Franceschi, U. Vrhovsek and F. Mattivi. Stability-based biomarker selection. Analytica Chimica Acta (2011), 705, 15-23. http://dx.doi.org/10.1016/j.aca.2011.01.039

Examples

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data(Apples)
## show features identified in all apples
plot(rt, mz,
     xlab = "Retention time (s)", ylab = "m/z",
     main = "Spiked apples - subset")