PLS Plot and Model creation Bug
Entering edit mode
thomas • 0
Last seen 4.1 years ago

Hi everybody,

New MAIT user but a seriously pleased one. What a game changer for my projects ... !


However, when few months ago, the full script was working OK, now I can't pass the PlotPLS and PLSModel lines.

This results in a 0kb graph file in the PLSScore plots folder with the following error message:

"Error: Please use column names for `x`"

I've tried, with my basic R knowledge, but can't figure out where this is from.

Anyone here having the same issue ? Any tips for fixing this ?

Many thanks !




R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] MAIT_1.9.0           pls_2.6-0            CAMERA_1.32.0        snow_0.4-2           xcms_1.52.0          MSnbase_2.2.0       
 [7] ProtGenerics_1.8.0   mzR_2.10.0           Rcpp_0.12.12         Biobase_2.36.2       BiocGenerics_0.22.0  doParallel_1.0.10   
[13] iterators_1.0.8      foreach_1.4.3        BiocParallel_1.10.1  BiocInstaller_1.26.0

loaded via a namespace (and not attached):
 [1] nlme_3.1-131           bitops_1.0-6           pbkrtest_0.4-7         plsgenomics_1.3-2      gmodels_2.16.2        
 [6] RColorBrewer_1.1-2     tools_3.4.0            backports_1.1.0        affyio_1.46.0          AlgDesign_1.1-7.3     
[11] rpart_4.1-11           KernSmooth_2.23-15     Hmisc_4.0-3            lazyeval_0.2.0         mgcv_1.8-19           
[16] colorspace_1.3-2       nnet_7.3-12            sp_1.2-5               gridExtra_2.2.1        klaR_0.6-12           
[21] compiler_3.4.0         MassSpecWavelet_1.42.0 preprocessCore_1.38.1  graph_1.54.0           quantreg_5.33         
[26] htmlTable_1.9          expm_0.999-2           SparseM_1.77           caTools_1.17.1         scales_0.5.0          
[31] checkmate_1.8.3        affy_1.54.0            RBGL_1.52.0            stringr_1.2.0          digest_0.6.12         
[36] foreign_0.8-69         minqa_1.2.4            base64enc_0.1-3        pkgconfig_2.0.1        htmltools_0.3.6       
[41] lme4_1.1-13            limma_3.32.5           htmlwidgets_0.9        rlang_0.1.2            impute_1.50.1         
[46] combinat_0.0-8         mzID_1.14.0            gtools_3.5.0           spdep_0.6-13           acepack_1.4.1         
[51] ModelMetrics_1.1.0     car_2.1-5              magrittr_1.5           Formula_1.2-2          MALDIquant_1.16.2     
[56] Matrix_1.2-11          munsell_0.4.3          S4Vectors_0.14.3       vsn_3.44.0             stringi_1.1.5         
[61] MASS_7.3-47            zlibbioc_1.22.0        gplots_3.0.1           plyr_1.8.4             grid_3.4.0            
[66] gdata_2.18.0           deldir_0.1-14          lattice_0.20-35        splines_3.4.0          multtest_2.32.0       
[71] knitr_1.17             igraph_1.1.2           boot_1.3-20            reshape2_1.4.2         codetools_0.2-15      
[76] stats4_3.4.0           LearnBayes_2.15        XML_3.98-1.9           latticeExtra_0.6-28    agricolae_1.2-6       
[81] pcaMethods_1.68.0      data.table_1.10.4      nloptr_1.0.4           MatrixModels_0.4-1     gtable_0.2.0          
[86] RANN_2.5.1             ggplot2_2.2.1          e1071_1.6-8            coda_0.19-1            class_7.3-14          
[91] survival_2.41-3        tibble_1.3.4           IRanges_2.10.2         cluster_2.0.6          caret_6.0-76          

MAIT PLS PLSDA PlotPLS PLSModel • 638 views

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