Dear all,
I am using caret package to analyze a microarray dataset with feature
selection using sbf(). My dataset is 3500 samples with 2200 genes, the
outcome Y variable is a factor of 12 levels. I used the following script to
run the feature selection:
library(caret)
ctrl <- sbfControl(functions=rfSBF, method='repeatedcv', repeats=5)
### x is a matrix of 3500x2200, y is a factor of 12 levels
obj <- sbf(x, y, sbfControl=ctrl)
But it has been more than 15 hours, the code is still running!
My computer has the following specifications:
Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz 2.00 GHz, 8 cores
16.0 GB
Does anyone know if my script has any issues, or it is normal for sbf() to
run this long?
Thank you!
Andrew
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] caret_6.0-94 lattice_0.21-8 ggplot2_3.4.2
loaded via a namespace (and not attached):
[1] utf8_1.2.3 future_1.33.0 generics_0.1.3
[4] class_7.3-22 stringi_1.7.12 pROC_1.18.2
[7] listenv_0.9.0 digest_0.6.32 magrittr_2.0.3
[10] grid_4.3.1 timechange_0.2.0 iterators_1.0.14
[13] foreach_1.5.2 plyr_1.8.8 Matrix_1.5-4.1
[16] ModelMetrics_1.2.2.2 nnet_7.3-19 survival_3.5-5
[19] purrr_1.0.1 fansi_1.0.4 scales_1.2.1
[22] codetools_0.2-19 lava_1.7.2.1 cli_3.6.1
[25] rlang_1.1.1 hardhat_1.3.0 parallelly_1.36.0
[28] future.apply_1.11.0 munsell_0.5.0 splines_4.3.1
[31] withr_2.5.0 prodlim_2023.03.31 tools_4.3.1
[34] parallel_4.3.1 reshape2_1.4.4 dplyr_1.1.2
[37] colorspace_2.1-0 recipes_1.0.6 globals_0.16.2
[40] vctrs_0.6.3 R6_2.5.1 rpart_4.1.19
[43] stats4_4.3.1 lifecycle_1.0.3 lubridate_1.9.2
[46] stringr_1.5.0 MASS_7.3-60 pkgconfig_2.0.3
[49] pillar_1.9.0 gtable_0.3.3 glue_1.6.2
[52] data.table_1.14.8 Rcpp_1.0.10 tibble_3.2.1
[55] tidyselect_1.2.0 nlme_3.1-162 ipred_0.9-14
[58] timeDate_4022.108 gower_1.0.1 compiler_4.3.1
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