Apples {RankProd} | R Documentation |
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.
data(Apples)
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) |
Francesco Del Carratore
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
data(Apples) ## show features identified in all apples plot(rt, mz, xlab = "Retention time (s)", ylab = "m/z", main = "Spiked apples - subset")