Hi! I am trying to run functional analysis with a list of “mz”, “rt”, and “p.value” with MetaboAnalystR. The input list is here:
48Hr_neg_MetaboAnalystR.txt (12.2 KB)
The pipeline I am using is as follows:
mSet_negative<-InitDataObjects(“mass_all”, “mummichog”, FALSE)
mSet_negative<-SetPeakFormat(mSet_negative,“mpr”)
mSet_negative<-UpdateInstrumentParameters(mSet_negative, 5.0, “negative”, “no”, 0.05);
mSet_negative<-Read.PeakListData(mSet_negative, “./48Hr_neg_MetaboAnalystR.txt”)
mSet_negative<-SetRTincluded(mSet_negative, “seconds”)
mSet_negative<-SanityCheckMummichogData(mSet_negative)
mSet_negative<-SetPeakEnrichMethod(mSet_negative, “mum”, “v2”)
mSet_negative<-SetMummichogPval(mSet_negative, 0.05)
mSet_negative<-PerformPSEA(mSet_negative, “hsa_kegg”, “current”, 3, 100)
Error message from PerformPSEA is as follows:
[1] “compoundLib”
[1] “Got 282 mass features.”
[1] “47 initial ECs created!”
Error in data.frame(value = unlist(try2), L1 = rep(try$L1, sapply(try2, :
arguments imply differing number of rows: 65, 0
I am wondering what exactly this means. Is the input list not long enough? The same input file works when SetPeakEnrichMethod is set to “v1” instead of “v2”.
Session info:
sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats4 splines grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] FELLA_1.24.0 pathview_1.44.0 MetaboAnalystR_4.0.0 MSnbase_2.30.1 ProtGenerics_1.36.0
[6] S4Vectors_0.42.1 mzR_2.38.0 fgsea_1.30.0 plotly_4.10.4 siggenes_1.78.0
[11] multtest_2.60.0 RColorBrewer_1.1-3 reshape_0.8.9 KEGGgraph_1.64.0 gplots_3.1.3.1
[16] caret_6.0-94 lattice_0.22-6 pls_2.8-4 xtable_1.8-4 magrittr_2.0.3
[21] Hmisc_5.1-3 lars_1.3 fitdistrplus_1.2-1 MASS_7.3-60.2 car_3.1-2
[26] carData_3.0-5 limma_3.60.4 data.table_1.15.4 pROC_1.18.5 Rcpp_1.0.13
[31] sva_3.52.0 mgcv_1.9-1 nlme_3.1-164 pheatmap_1.0.12 genefilter_1.86.0
[36] preprocessCore_1.66.0 Rgraphviz_2.48.0 graph_1.82.0 GlobalAncova_4.22.0 corpcor_1.6.10
[41] globaltest_5.58.0 survival_3.6-4 ROCR_1.0-11 RJSONIO_1.3-1.9 pcaMethods_1.96.0
[46] Biobase_2.64.0 BiocGenerics_0.50.0 impute_1.78.0 som_0.3-5.1 e1071_1.7-14
[51] caTools_1.18.2 randomForest_4.7-1.1 Cairo_1.6-2 scatterplot3d_0.3-44 ellipse_0.5.0
[56] Rserve_1.8-13 pacman_0.5.1 httr_1.4.7 igraph_2.0.3 lubridate_1.9.3
[61] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5 tibble_3.2.1
[66] tidyverse_2.0.0 plyr_1.8.9 readxl_1.4.3 DT_0.33 ggplot2_3.5.1
[71] writexl_1.5.0 tidyr_1.3.1 dplyr_1.1.4 xcms_4.2.2 BiocParallel_1.38.0
[76] shiny_1.9.1
loaded via a namespace (and not attached):
[1] IRanges_2.38.1 GSEABase_1.66.0 progress_1.2.3 vsn_3.72.0
[5] urlchecker_1.0.1 nnet_7.3-19 Biostrings_2.72.1 vctrs_0.6.5
[9] RApiSerialize_0.1.3 digest_0.6.36 png_0.1-8 proxy_0.4-27
[13] parallelly_1.38.0 reshape2_1.4.4 httpuv_1.6.15 foreach_1.5.2
[17] withr_3.0.1 xfun_0.46 ellipsis_0.3.2 MetaboCoreUtils_1.12.0
[21] memoise_2.0.1 profvis_0.3.8 gtools_3.9.5 Formula_1.2-5
[25] prettyunits_1.2.0 KEGGREST_1.44.1 promises_1.3.0 globals_0.16.3
[29] ps_1.7.7 stringfish_0.16.0 rstudioapi_0.16.0 UCSC.utils_1.0.0
[33] miniUI_0.1.1.1 generics_0.1.3 base64enc_0.1-3 MassSpecWavelet_1.70.0
[37] processx_3.8.4 curl_5.2.1 ncdf4_1.22 zlibbioc_1.50.0
[41] GenomeInfoDbData_1.2.12 SparseArray_1.4.8 desc_1.4.3 doParallel_1.0.17
[45] evaluate_0.24.0 S4Arrays_1.4.1 hms_1.1.3 GenomicRanges_1.56.1
[49] qs_0.26.3 colorspace_2.1-1 later_1.3.2 viridis_0.6.5
[53] MsCoreUtils_1.16.1 future.apply_1.11.2 XML_3.99-0.17 cowplot_1.1.3
[57] matrixStats_1.3.0 class_7.3-22 pillar_1.9.0 iterators_1.0.14
[61] compiler_4.4.1 stringi_1.8.4 gower_1.0.1 SummarizedExperiment_1.34.0
[65] dendextend_1.17.1 devtools_2.4.5 crayon_1.5.3 abind_1.4-5
[69] locfit_1.5-9.10 org.Hs.eg.db_3.19.1 bit_4.0.5 fastmatch_1.1-4
[73] codetools_0.2-20 recipes_1.1.0 crosstalk_1.2.1 bslib_0.8.0
[77] mime_0.12 MultiAssayExperiment_1.30.3 cellranger_1.1.0 knitr_1.48
[81] blob_1.2.4 utf8_1.2.4 clue_0.3-65 AnnotationFilter_1.28.0
[85] fs_1.6.4 QFeatures_1.14.2 listenv_0.9.1 mzID_1.42.0
[89] checkmate_2.3.2 pkgbuild_1.4.4 Matrix_1.7-0 callr_3.7.6
[93] statmod_1.5.0 tzdb_0.4.0 pkgconfig_2.0.3 tools_4.4.1
[97] cachem_1.1.0 RSQLite_2.3.7 viridisLite_0.4.2 DBI_1.2.3
[101] fastmap_1.2.0 rmarkdown_2.27 scales_1.3.0 crmn_0.0.21
[105] usethis_3.0.0 sass_0.4.9 BiocManager_1.30.23 scrime_1.3.5
[109] rpart_4.1.23 yaml_2.3.10 VGAM_1.1-11 MatrixGenerics_1.16.0
[113] foreign_0.8-86 cli_3.6.3 lifecycle_1.0.4 lava_1.8.0
[117] sessioninfo_1.2.2 backports_1.5.0 annotate_1.82.0 timechange_0.3.0
[121] gtable_0.3.5 parallel_4.4.1 jsonlite_1.8.8 edgeR_4.2.1
[125] bitops_1.0-8 bit64_4.0.5 glasso_1.11 MsExperiment_1.6.0
[129] RcppParallel_5.1.8 jquerylib_0.1.4 timeDate_4032.109 lazyeval_0.2.2
[133] htmltools_0.5.8.1 affy_1.82.0 glue_1.7.0 XVector_0.44.0
[137] RCurl_1.98-1.16 MALDIquant_1.22.2 gridExtra_2.3 R6_2.5.1
[141] cluster_2.1.6 pkgload_1.4.0 Spectra_1.14.1 GenomeInfoDb_1.40.1
[145] ipred_0.9-15 DelayedArray_0.30.1 tidyselect_1.2.1 htmlTable_2.4.3
[149] AnnotationDbi_1.66.0 future_1.34.0 MsFeatures_1.12.0 ModelMetrics_1.2.2.2
[153] munsell_0.5.1 KernSmooth_2.23-24 affyio_1.74.0 htmlwidgets_1.6.4
[157] rlang_1.1.4 remotes_2.5.0 fansi_1.0.6 hardhat_1.4.0
[161] prodlim_2024.06.25 PSMatch_1.8.0
Thank you very much