Frank Koopmans ftwkoopmans
ftwkoopmans
/ msempire_reproducibility_needs_set-seed.R
Created
February 9, 2020 00:53
demonstrate lack of MS-EmpiRe reproducibility when set.seed() is not used
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # code snippet to demonstrate MS-EmpiRe reproducibility issues & resolve by setting set.seed() | |
| # msEmpiRe package build used for this testcase: https://github.com/zimmerlab/MS-EmpiRe/tree/ae985a92dada3ea6bce9ee88e6eb674ffe975f41 | |
| # author: Frank Koopmans, Department of Molecular and Cellular Neurobiology, VU University, Amsterdam, The Netherlands | |
| library(msEmpiRe) | |
| ### example dataset and application of MS-EmpiRe following the documentation at: https://github.com/zimmerlab/MS-EmpiRe/blob/master/example.R | |
| f <- system.file("extdata", "c1_c3.data", package = "msEmpiRe") | |
| p <- system.file("extdata", "c1_c3.pdata", package = "msEmpiRe") | |
| # loading data from installed data sets. The dataset is the yeast spike-in benchmarking data of O'Connell et al., as discussed in the paper |