jorainer
commented
3 weeks ago Sorry for my late reply. This is a bit surprising, because if you follow the steps in the xcms package you referenced above (which is this one, and refers to version 4.2.3 of xcms) the faahko variable should be a XcmsExperiment object, not a xcmsSet object. Can it be that the faahko variable you loaded/used is from an old version of the package?
Hi,
I am running your tutorial (https://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html#6_Session_information), and met a problem when I run the code
spectra(faahko). The error message is as follows: "Error: unable to find an inherited method for function ‘spectra’ for signature ‘object = "xcmsSet".Besides, when I run
faahko, the output is as follows:My sessionInfo() is as follows: """ R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1
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: Asia/Hong_Kong tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] MsExperiment_1.6.0 ProtGenerics_1.36.0 pheatmap_1.0.12
[4] pander_0.6.5 RColorBrewer_1.1-3 faahKO_1.44.0
[7] xcms_4.2.3 BiocParallel_1.38.0
loaded via a namespace (and not attached): [1] DBI_1.2.3 rlang_1.1.4
[3] magrittr_2.0.3 clue_0.3-65
[5] MassSpecWavelet_1.70.0 matrixStats_1.3.0
[7] compiler_4.4.1 vctrs_0.6.5
[9] reshape2_1.4.4 stringr_1.5.1
[11] pkgconfig_2.0.3 MetaboCoreUtils_1.12.0
[13] crayon_1.5.3 XVector_0.44.0
[15] utf8_1.2.4 UCSC.utils_1.0.0
[17] preprocessCore_1.66.0 purrr_1.0.2
[19] MultiAssayExperiment_1.30.3 zlibbioc_1.50.0
[21] GenomeInfoDb_1.40.1 jsonlite_1.8.8
[23] progress_1.2.3 DelayedArray_0.30.1
[25] parallel_4.4.1 prettyunits_1.2.0
[27] cluster_2.1.6 R6_2.5.1
[29] stringi_1.8.4 limma_3.60.4
[31] GenomicRanges_1.56.1 Rcpp_1.0.13
[33] SummarizedExperiment_1.34.0 iterators_1.0.14
[35] IRanges_2.38.1 Matrix_1.7-0
[37] igraph_2.0.3 tidyselect_1.2.1
[39] abind_1.4-5 doParallel_1.0.17
[41] codetools_0.2-20 affy_1.82.0
[43] lattice_0.22-6 tibble_3.2.1
[45] plyr_1.8.9 Biobase_2.64.0
[47] Spectra_1.14.1 pillar_1.9.0
[49] affyio_1.74.0 BiocManager_1.30.25
[51] MatrixGenerics_1.16.0 foreach_1.5.2
[53] stats4_4.4.1 MSnbase_2.30.1
[55] MALDIquant_1.22.3 ncdf4_1.23
[57] generics_0.1.3 S4Vectors_0.42.1
[59] hms_1.1.3 ggplot2_3.5.1
[61] munsell_0.5.1 scales_1.3.0
[63] glue_1.7.0 MsFeatures_1.12.0
[65] lazyeval_0.2.2 tools_4.4.1
[67] mzID_1.42.0 QFeatures_1.14.2
[69] vsn_3.72.0 mzR_2.38.0
[71] fs_1.6.4 XML_3.99-0.17
[73] grid_4.4.1 impute_1.78.0
[75] tidyr_1.3.1 MsCoreUtils_1.16.1
[77] colorspace_2.1-1 GenomeInfoDbData_1.2.12
[79] PSMatch_1.8.0 cli_3.6.3
[81] fansi_1.0.6 S4Arrays_1.4.1
[83] dplyr_1.1.4 AnnotationFilter_1.28.0
[85] pcaMethods_1.96.0 gtable_0.3.5
[87] digest_0.6.37 BiocGenerics_0.50.0
[89] SparseArray_1.4.8 lifecycle_1.0.4
[91] httr_1.4.7 statmod_1.5.0
[93] MASS_7.3-61
"""
Many thanks for your help.