BC: Three metabolomics data sets for Arabidopsis

In rwehrens/BatchCorrMetabolomics: Complementary package to "Improved Batch Correction in Untargeted MS-Based Metabolomics"

Description

Three real-life data sets are provided for testing batch correction procedures, all three from Arabidopsis thaliana samples. In each case, the data object (set.1, set.2 or set.3) contains relative intensities of reconstructed metabolites (columns) for a number of samples (rows). The corresponding meta-information object (set.1.Y, set.2.Y, set.3.Y, respectively) contains for every sample batch and sequence information, as well as (coded) information on the genotype and the sample type (study sample or reference sample). Processing of the raw data has been done with Metalign and MSClust programs.

Usage

data(BC)

Details

Set 1: data from a set of 761 injections containing 51 QC samples and biological replicates of 357 natural Arabidopsis thaliana accessions. Number of metabolites: 567 reconstructed metabolites.

Set 2: data from a set of 753 injections containing 50 QC samples and biological replicates of 357 natural Arabidopsis thaliana accessions (same as set.1). Number of metabolites: 603.

Set 3: Data from a set of 240 injections containing 14 QC samples and biological replicates of 58 Arabidopsis thaliana accessions. Number of metabolites: 75.

References

"@ArticleWehrens2016, author = Ron Wehrens and Jos.~A.~Hageman and Fred~van~Eeuwijk and Rik~Kooke and P\'adraic~J.~Flood and Erik Wijnker and Joost~J.B.~Keurentjes and Arjen~Lommen and Henri\"ette~D.L.M.~van~Eekelen and Robert~D.~Hall and Roland~Mumm and Ric~C.H.~de~Vos, title = Improved batch correction in untargeted MS-based metabolomics, journal = Metabolomics, year = 2016, volume = 12, DOI = 10.1007/s11306-016-1015-8, pages = 1–12 "

Examples

data(BC)
dim(set.1)
sum(is.na(set.1))
dim(set.1.Y)

dim(set.2)
sum(is.na(set.2))
dim(set.2.Y)

dim(set.3)
sum(is.na(set.3))
dim(set.3.Y)

rwehrens/BatchCorrMetabolomics documentation built on May 28, 2019, 10:42 a.m.