dont find xcmsSet for peak analysis
0
0
Entering edit mode
@5e08d646
Last seen 2.2 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 • 552 views
ADD COMMENT

Login before adding your answer.

Traffic: 816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6