Hi “@ everyone”!
I have a problem regarding MetaboAnalystR data input.
I want to input a *.zip with *.csv files divided in groups subfolders just as MetaboAnalyst PeakLists MS Format.
The problem is that it does not recognize correctly the command Read.PeakList, because the SanityCheck I do immediately afterwards gives an error and I can’t continue afterwards. I am currently using the PeakList example ‘lcms_3col_peaks.zip’ and this is my code. Data is already unzipped into ‘upload folder’:
> library("MetaboAnalystR")
MetaboAnalystR 4.0.0 initialized Successfully !
https://github.com/xia-lab/MetaboAnalystR
> mSet<-InitDataObjects("mspeak", "stat", FALSE)
Starting Rserve...
"C:\Users\IPLA-T~1\AppData\Local\R\WIN-LI~1\4.4\Rserve\libs\x64\Rserve.exe" --no-save
[1] "MetaboAnalyst R objects initialized ..."
Aviso:
In Cairo::CairoFonts(regular = "Arial:style=Regular", bold = "Arial:style=Bold", :
CairoFonts() has no effect on Windows. Please use par(family="...") to specify the desired font - see ?par.
> getwd()
[1] "C:/Users/IPLA-Thinkpad2024/Documents"
> setwd('./WorkFolder/MetaboAnalystR_Proforma/Comparación_Estadísticas_MetaboAnalyst/ParaMetaboAnalystR')
> mSet<-Read.PeakList(mSet,"upload")
> mSet<-SanityCheckData(mSet)
[1] "A total of 0 groups found with 0 samples."
[1] "<font color='red'>At least <b>two</b> groups and <b>three replicates</b> per group are required for analysis</font>!"
[1] "You can click the <b>Edit Groups</b> button below to see the group labels for each sample and make corrections."
Aviso:
In min(table(cls.Clean)) : ningún argumento finito para min; retornando Inf
> mSet
[1] -1
> mSet<-Read.PeakList(mSet,"upload")
Error en `*tmp*`$msgSet: $ operator is invalid for atomic vectors
> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Spain.utf8 LC_CTYPE=Spanish_Spain.utf8
[3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.utf8
time zone: Europe/Madrid
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rserve_1.8-13 MetaboAnalystR_4.0.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3
[4] fs_1.6.4 vctrs_0.6.5 multtest_2.60.0
[7] memoise_2.0.1 Cairo_1.6-2 htmltools_0.5.8.1
[10] usethis_3.0.0 curl_5.2.3 pROC_1.18.5
[13] caret_6.0-94 parallelly_1.38.0 KernSmooth_2.23-24
[16] htmlwidgets_1.6.4 desc_1.4.3 plyr_1.8.9
[19] impute_1.78.0 plotly_4.10.4 lubridate_1.9.3
[22] cachem_1.1.0 igraph_2.0.3 mime_0.12
[25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[28] Matrix_1.7-0 R6_2.5.1 fastmap_1.2.0
[31] future_1.34.0 shiny_1.9.1 digest_0.6.37
[34] pcaMethods_1.96.0 colorspace_2.1-1 siggenes_1.78.0
[37] ps_1.8.0 pkgload_1.4.0 RSQLite_2.3.7
[40] fansi_1.0.6 timechange_0.3.0 httr_1.4.7
[43] compiler_4.4.1 remotes_2.5.0 bit64_4.5.2
[46] withr_3.0.1 glasso_1.11 BiocParallel_1.38.0
[49] DBI_1.2.3 qs_0.26.3 pkgbuild_1.4.4
[52] gplots_3.1.3.1 MASS_7.3-61 lava_1.8.0
[55] sessioninfo_1.2.2 gtools_3.9.5 caTools_1.18.3
[58] ModelMetrics_1.2.2.2 tools_4.4.1 httpuv_1.6.15
[61] future.apply_1.11.2 nnet_7.3-19 glue_1.7.0
[64] callr_3.7.6 nlme_3.1-166 promises_1.3.0
[67] grid_4.4.1 reshape2_1.4.4 fgsea_1.30.0
[70] generics_0.1.3 recipes_1.1.0 gtable_0.3.5
[73] class_7.3-22 tidyr_1.3.1 data.table_1.16.0
[76] RApiSerialize_0.1.4 stringfish_0.16.0 utf8_1.2.4
[79] BiocGenerics_0.50.0 foreach_1.5.2 pillar_1.9.0
[82] stringr_1.5.1 limma_3.60.4 later_1.3.2
[85] splines_4.4.1 dplyr_1.1.4 lattice_0.22-6
[88] survival_3.7-0 bit_4.5.0 tidyselect_1.2.1
[91] locfit_1.5-9.10 miniUI_0.1.1.1 edgeR_4.2.1
[94] stats4_4.4.1 Biobase_2.64.0 scrime_1.3.5
[97] statmod_1.5.0 hardhat_1.4.0 devtools_2.4.5
[100] timeDate_4041.110 stringi_1.8.4 lazyeval_0.2.2
[103] codetools_0.2-20 crmn_0.0.21 tibble_3.2.1
[106] BiocManager_1.30.25 cli_3.6.3 RcppParallel_5.1.9
[109] rpart_4.1.23 xtable_1.8-4 munsell_0.5.1
[112] processx_3.8.4 Rcpp_1.0.13 globals_0.16.3
[115] parallel_4.4.1 ellipsis_0.3.2 gower_1.0.1
[118] ggplot2_3.5.1 blob_1.2.4 profvis_0.4.0
[121] urlchecker_1.0.1 bitops_1.0-8 listenv_0.9.1
[124] viridisLite_0.4.2 ipred_0.9-15 scales_1.3.0
[127] prodlim_2024.06.25 purrr_1.0.2 rlang_1.1.4
[130] cowplot_1.1.3 fastmatch_1.1-4
Any ideas how to evade this MetaboAnalystR bug?
Thanks in advance!