I am attempting to remove the batch effect using “QC-RLSC” in MetaboAnalystR.
However, it keeps indicating that the format is incorrect.
I have also tried using the website version, but it presents similar issues.
I have double-checked the format by following the guide on the website.
(Refer to the “Question mark” beside “Please upload your data table”, under the “Upload a single merged file” section)
Could you assist me in identifying the error in my data table?
Detail info
- Which tool and which module
MetaboAnalystR 4.0.0 on R version 4.3.2 (Windows 11) - Provide a copy of your data (actual data that leads to the error, not a screenshot image of the data), or indicate which example data you used
QC_sample_subset3.csv (16.2 KB)
QC_sample_subset3.txt (38.0 KB) - Document all steps leading to the issue. Sometimes screenshots may be necessary
>library(MetaboAnalystR)
MetaboAnalystR 4.0.0 initialized Successfully !
https://github.com/xia-lab/MetaboAnalystR
> mSet <- InitDataObjects("pktable", "utils", FALSE)
[1] "MetaboAnalyst R objects initialized ..."
Warning message:
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.
> mSet <- Read.BatchDataTB(mSet, "QC_sample_subset3.csv", "row", "KNN")
missing value estimate: KNN
> mSet <- PerformBatchCorrection(mSet)
[1] "Correcting using the auto method !"
[1] "Correcting with Combat..."
[1] "Correcting with WaveICA..."
[1] "Correcting with EigenMS..."
[1] "Correcting with QC-RLSC..."
[1] "Your data or format is not valid! Please double check!"
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
3: In serialize(data, node$con) :
'package:stats' may not be available when loading
4: In serialize(data, node$con) :
'package:stats' may not be available when loading
5: In serialize(data, node$con) :
'package:stats' may not be available when loading
6: In serialize(data, node$con) :
'package:stats' may not be available when loading
- If it is about using R packages, you also need to provide the environment information
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_Malaysia.utf8 LC_CTYPE=English_Malaysia.utf8 LC_MONETARY=English_Malaysia.utf8
[4] LC_NUMERIC=C LC_TIME=English_Malaysia.utf8
time zone: Asia/Kuala_Lumpur
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MetaboAnalystR_4.0.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-8 pROC_1.18.5 rlang_1.1.4
[5] magrittr_2.0.3 scrime_1.3.5 matrixStats_1.3.0 compiler_4.3.2
[9] RSQLite_2.3.7 mgcv_1.9-0 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 sva_3.50.0 stringr_1.5.1 crayon_1.5.3
[17] pkgconfig_2.0.3 fastmap_1.2.0 XVector_0.42.0 caTools_1.18.2
[21] utf8_1.2.4 prodlim_2024.06.25 purrr_1.0.2 bit_4.0.5
[25] zlibbioc_1.48.2 cachem_1.1.0 GenomeInfoDb_1.38.8 jsonlite_1.8.8
[29] recipes_1.1.0 blob_1.2.4 BiocParallel_1.36.0 parallel_4.3.2
[33] R6_2.5.1 stringi_1.8.4 RColorBrewer_1.1-3 genefilter_1.84.0
[37] qs_0.26.3 limma_3.58.1 parallelly_1.38.0 rpart_4.1.21
[41] lubridate_1.9.3 Rcpp_1.0.13 iterators_1.0.14 future.apply_1.11.2
[45] snow_0.4-4 IRanges_2.36.0 Matrix_1.6-1.1 splines_4.3.2
[49] nnet_7.3-19 igraph_2.0.3 timechange_0.3.0 tidyselect_1.2.1
[53] rstudioapi_0.16.0 stringfish_0.16.0 siggenes_1.76.0 timeDate_4032.109
[57] gplots_3.1.3.1 codetools_0.2-19 listenv_0.9.1 lattice_0.21-9
[61] tibble_3.2.1 plyr_1.8.9 KEGGREST_1.42.0 Biobase_2.62.0
[65] withr_3.0.1 future_1.34.0 survival_3.5-7 RcppParallel_5.1.8
[69] Biostrings_2.70.3 pillar_1.9.0 MatrixGenerics_1.14.0 KernSmooth_2.23-22
[73] foreach_1.5.2 stats4_4.3.2 plotly_4.10.4 generics_0.1.3
[77] RCurl_1.98-1.16 S4Vectors_0.40.2 ggplot2_3.5.1 munsell_0.5.1
[81] scales_1.3.0 RApiSerialize_0.1.3 xtable_1.8-4 gtools_3.9.5
[85] globals_0.16.3 class_7.3-22 glue_1.7.0 lazyeval_0.2.2
[89] tools_4.3.2 data.table_1.15.4 annotate_1.80.0 ModelMetrics_1.2.2.2
[93] fgsea_1.28.0 gower_1.0.1 locfit_1.5-9.10 XML_3.99-0.17
[97] fastmatch_1.1-4 cowplot_1.1.3 grid_4.3.2 Cairo_1.6-2
[101] impute_1.76.0 tidyr_1.3.1 AnnotationDbi_1.64.1 ipred_0.9-15
[105] edgeR_4.0.16 colorspace_2.1-1 GenomeInfoDbData_1.2.11 nlme_3.1-163
[109] crmn_0.0.21 cli_3.6.3 fansi_1.0.6 viridisLite_0.4.2
[113] lava_1.8.0 dplyr_1.1.4 glasso_1.11 pcaMethods_1.94.0
[117] gtable_0.3.5 digest_0.6.36 BiocGenerics_0.48.1 caret_6.0-94
[121] htmlwidgets_1.6.4 htmltools_0.5.8.1 memoise_2.0.1 multtest_2.58.0
[125] lifecycle_1.0.4 httr_1.4.7 hardhat_1.4.0 statmod_1.5.0
[129] bit64_4.0.5 MASS_7.3-60