Hello, I am trying to use “DDA MS/MS data processing” in MetaboAnalystR searching MS/MS reference library, the “MS2ID_Lipids_v09102023.sqlite” database was used.
In the tutorial: LC-MS/MS Raw Spectral Data Processing
“If the dataset is a lipidomics dataset, please set 3rd argument as “TRUE””,
10). SuperClass_N, Superclass of the Nth identification (only for lipidomics database).
11). MainClass_N, Mainclass of the Nth identification (only for lipidomics database).
12). SubClass_N, Subclass of the Nth identification (only for lipidomics database).
however, I consistently get the error below, please help to check it, Tx.
3.6 Results export
mSet ← PerformResultsExport (mSet,
-
type = 0L, -
topN = 10L, -
ncores = 6L, -
lipids = TRUE - )
======= Converting started. See progress below =======
…
============ Exporting finished successfully! ============
dtx ← FormatMSnAnnotation(mSet, 5L, TRUE)
Error in data.frame(cmpds = cmpds[idx], inchikeys = inchikeys[idx], formulas = formulas[idx], :
arguments imply differing number of rows: 0, 1
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /share/software/user/open/openblas/0.3.10/lib/libopenblas_haswellp-r0.3.10.so
locale:
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] OptiLCMS_1.1.0 MSnbase_2.24.2 ProtGenerics_1.30.0 S4Vectors_0.36.2 mzR_2.32.0 Rcpp_1.0.11
[7] BiocParallel_1.32.6 Biobase_2.58.0 BiocGenerics_0.44.0 MetaboAnalystR_4.0.0