Error received in ropls package
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@82b19035
Last seen 11 days ago
Ireland

I am trying to run the ropls packahe but get this error even with the sample data. Can you let me know how to resolve this error?

Code should be placed in three backticks as shown below


>sacurine.oplsda <- opls(dataMatrix, genderFc, predI = 1, orthoI = NA, subset = "odd")
trainVi <- sacurine.oplsda[["subset"]]
Error in sacurine.oplsda[["subset"]] : this S4 class is not subsettable

sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=es_ES.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=es_ES.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ropls_1.28.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9                  XVector_0.36.0              GenomeInfoDb_1.32.4         pillar_1.8.1               
 [5] compiler_4.2.0              MatrixGenerics_1.8.1        zlibbioc_1.42.0             bitops_1.0-7               
 [9] base64enc_0.1-3             keras_2.9.0                 tools_4.2.0                 MultiDataSet_1.24.0        
[13] zeallot_0.1.0               jsonlite_1.8.3              lifecycle_1.0.3             tibble_3.1.8               
[17] lattice_0.20-45             pkgconfig_2.0.3             png_0.1-7                   rlang_1.0.6                
[21] Matrix_1.5-1                DelayedArray_0.22.0         cli_3.4.1                   DBI_1.1.3                  
[25] rstudioapi_0.14             qqman_0.1.8                 GenomeInfoDbData_1.2.8      dplyr_1.0.10               
[29] IRanges_2.30.1              S4Vectors_0.34.0            generics_0.1.3              vctrs_0.5.0                
[33] rappdirs_0.3.3              stats4_4.2.0                rprojroot_2.0.3             MultiAssayExperiment_1.22.0
[37] grid_4.2.0                  tidyselect_1.2.0            calibrate_1.7.7             reticulate_1.26            
[41] glue_1.6.2                  Biobase_2.56.0              here_1.0.1                  R6_2.5.1                   
[45] fansi_1.0.3                 limma_3.52.4                magrittr_2.0.3              whisker_0.4                
[49] MASS_7.3-58.1               matrixStats_0.62.0          tfruns_1.5.1                BiocGenerics_0.42.0        
[53] GenomicRanges_1.48.0        SummarizedExperiment_1.26.1 assertthat_0.2.1            tensorflow_2.9.0           
[57] utf8_1.2.2                  RCurl_1.98-1.9
Metabolomics ropls • 86 views
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What is your data and what do you want to do ?

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@etiennethevenot-8285
Last seen 6 days ago
France

Hi, As described in the vignette, the correct command line to get the indices of the training samples is:

trainVi <- getSubsetVi(sacurine.oplsda)

Best, Etienne.

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