MSstats Error: Must specify either `data` or `newdata` argument.
https://gitlab.bfabric.org/cpanse/timstof/-/blob/master/R/MSstats_dataProcessing.R#L66
error when running
[bfabric@fgcz-r-033:WU254482]$ pwd
/export/data01/MSSTATS/WU254482
[bfabric@fgcz-r-033:WU254482]$ R --no-save < MSstats_dataProcessing.R
+ featureSubset = parameters$prefix_featureSubset,
+ remove_uninformative_feature_outlier = as.logical(parameters$prefix_remove_uninformative_feature_outlier),
+ summaryMethod = parameters$prefix_summaryMethod,
+ equalFeatureVar = as.logical(parameters$prefix_equalFeatureVar),
+ MBimpute = as.logical(parameters$prefix_MBimpute)
+ )
** Flag uninformative feature and outliers by feature selection algorithm.
Analyzing features in L channel...
Joining, by = c("protein", "feature")
Joining, by = "protein"
Joining, by = "protein"
Identifying low-coverage features...
Fitting robust linear models...
Joining, by = "protein"
Identifying outliers and calculating feature variances...
Error: Must specify either `data` or `newdata` argument.
In addition: Warning message:
124 very small variances detected, have been offset away from zero
Execution halted