dont find xcmsSet for peak analysis
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@5e08d646
Last seen 2.1 years ago
Germany

I am coding and this xcmsSet is not running.... Could you help me, please

```xset <- xcmsSet(files=coffees, mzdiff=0.2, fwhm=5, step=0.1, snthresh=5) Warning messages: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In serialize(data, node$con) : 'package:stats' may not be available when loading

```sessionInfo( ) R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats4 stats graphics grDevices utils
[6] datasets methods base

other attached packages: [1] CAMERA_1.52.0 xcms_3.18.0
[3] MSnbase_2.22.0 ProtGenerics_1.28.0 [5] S4Vectors_0.34.0 mzR_2.30.0
[7] Rcpp_1.0.9 Biobase_2.56.0
[9] BiocGenerics_0.42.0 BiocParallel_1.30.3 [11] tidytext_0.3.4 forcats_0.5.2
[13] stringr_1.4.1 dplyr_1.0.10
[15] purrr_0.3.5 readr_2.1.3
[17] tidyr_1.2.1 tibble_3.1.8
[19] ggplot2_3.3.6 tidyverse_1.3.2
[21] BiocManager_1.30.18

loaded via a namespace (and not attached): [1] googledrive_2.0.0
[2] colorspace_2.0-3
[3] deldir_1.0-6
[4] ellipsis_0.3.2
[5] htmlTable_2.4.1
[6] XVector_0.36.0
[7] base64enc_0.1-3
[8] GenomicRanges_1.48.0
[9] fs_1.5.2
[10] clue_0.3-61
[11] rstudioapi_0.14
[12] affyio_1.66.0
[13] SnowballC_0.7.0
[14] fansi_1.0.3
[15] lubridate_1.8.0
[16] xml2_1.3.3
[17] splines_4.2.1
[18] codetools_0.2-18
[19] ncdf4_1.19
[20] doParallel_1.0.17
[21] impute_1.70.0
[22] robustbase_0.95-0
[23] knitr_1.40
[24] Formula_1.2-4
[25] jsonlite_1.8.2
[26] broom_1.0.1
[27] cluster_2.1.4
[28] vsn_3.64.0
[29] dbplyr_2.2.1
[30] png_0.1-7
[31] graph_1.74.0
[32] compiler_4.2.1
[33] httr_1.4.4
[34] backports_1.4.1
[35] fastmap_1.1.0
[36] assertthat_0.2.1
[37] Matrix_1.5-1
[38] gargle_1.2.1
[39] limma_3.52.4
[40] cli_3.4.1
[41] htmltools_0.5.3
[42] tools_4.2.1
[43] igraph_1.3.5
[44] gtable_0.3.1
[45] glue_1.6.2
[46] GenomeInfoDbData_1.2.8
[47] affy_1.74.0
[48] RANN_2.6.1
[49] tinytex_0.42
[50] MALDIquant_1.21
[51] cellranger_1.1.0
[52] vctrs_0.4.2
[53] preprocessCore_1.58.0
[54] iterators_1.0.14
[55] xfun_0.33
[56] rvest_1.0.3
[57] lifecycle_1.0.3
[58] XML_3.99-0.11
[59] googlesheets4_1.0.1
[60] DEoptimR_1.0-11
[61] zlibbioc_1.42.0
[62] MASS_7.3-58.1
[63] scales_1.2.1
[64] pcaMethods_1.88.0
[65] hms_1.1.2
[66] MatrixGenerics_1.8.1
[67] parallel_4.2.1
[68] SummarizedExperiment_1.26.1 [69] RBGL_1.72.0
[70] MassSpecWavelet_1.62.0
[71] RColorBrewer_1.1-3
[72] gridExtra_2.3
[73] MsFeatures_1.4.0
[74] rpart_4.1.16
[75] latticeExtra_0.6-30
[76] stringi_1.7.8
[77] tokenizers_0.2.3
[78] foreach_1.5.2
[79] checkmate_2.1.0
[80] GenomeInfoDb_1.32.4
[81] rlang_1.0.6
[82] pkgconfig_2.0.3
[83] matrixStats_0.62.0
[84] bitops_1.0-7
[85] mzID_1.34.0
[86] lattice_0.20-45
[87] htmlwidgets_1.5.4
[88] tidyselect_1.2.0
[89] plyr_1.8.7
[90] magrittr_2.0.3
[91] R6_2.5.1
[92] snow_0.4-4
[93] Hmisc_4.7-1
[94] IRanges_2.30.1
[95] generics_0.1.3
[96] DelayedArray_0.22.0
[97] DBI_1.1.3
[98] foreign_0.8-83
[99] pillar_1.8.1
[100] haven_2.5.1
[101] withr_2.5.0
[102] MsCoreUtils_1.8.0
[103] nnet_7.3-18
[104] survival_3.4-0
[105] RCurl_1.98-1.9
[106] janeaustenr_1.0.0
[107] modelr_0.1.9
[108] crayon_1.5.2
[109] interp_1.1-3
[110] utf8_1.2.2
[111] tzdb_0.3.0
[112] jpeg_0.1-9
[113] grid_4.2.1
[114] readxl_1.4.1
[115] data.table_1.14.2
[116] reprex_2.0.2
[117] digest_0.6.29
[118] munsell_0.5.0

I substitute the Rversion and that popped up....

'''xset <- xcmsSet(files=coffees, mzdiff=0.2, fwhm=5, step=0.1, snthresh=5) Error in xcmsSet(files = coffees, mzdiff = 0.2, fwhm = 5, step = 0.1, : could not find function "xcmsSet"

sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats4 parallel stats graphics grDevices [6] utils datasets methods base

other attached packages: [1] XVector_0.30.0 IRanges_2.24.1
[3] ProtGenerics_1.22.0 S4Vectors_0.28.1
[5] mzR_2.24.1 Rcpp_1.0.8.3
[7] BiocParallel_1.24.1 Biobase_2.50.0
[9] BiocGenerics_0.36.1

loaded via a namespace (and not attached): [1] codetools_0.2-18 grid_4.0.4
[3] ncdf4_1.19 zlibbioc_1.36.0
[5] impute_1.64.0 tools_4.0.4
[7] compiler_4.0.4 BiocManager_1.30.18

Best Regards Aline

xcms • 540 views
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