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Published
20 hours ago •
mixOmicsTeam
mixOmicsTeam
`perf()` on `pls` unable to handle near zero variance features
🐞 Describe the bug:
When running the perf() function on a pls object (using any PLS mode), if there are features which have near zero variance (nzv), the following error is raised:
Error in Ypred[omit, , h] <- Y.hat[, , 1] :
number of items to replace is not a multiple of replacement length
This pub was raised by two users on the discourse forum: https://mixomics-users.discourse.group/t/pls-and-diablo-tuning/742/4
🔍 reprex results from reproducible example including sessioninfo():
library(mixOmics)
data("liver.toxicity")
# reducing number of features to reduce run time
X <- liver.toxicity$gene[, 1:1000]
Y <- liver.toxicity$clinic
# to reproduce error, we need to induce some features to have near zero variance
X[, c(1, 23, 62, 234, 789)] <- 0
pls.obg <- pls(Y, X, ncomp = 4)
#> Warning in cor(A[[k]], variates.A[[k]]): the standard deviation is zero
pls.perf.obj <- perf(pls.obg, validation = "Mfold", folds = 4,
progressBar = F,
nrepeat = 3)
#> Error in Ypred[omit, , h] <- Y.hat[, , 1]: number of items to replace is not a multiple of replacement length
Created on 2022-03-28 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
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#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_Australia.1252
#> ctype English_Australia.1252
#> tz Australia/Sydney
#> date 2022-03-28
#> pandoc 2.14.2 @ C:/Users/Work/AppData/Local/Pandoc/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.3)
#> BiocParallel 1.28.3 2021-12-09 [1] Bioconductor
#> cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2)
#> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
#> corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.1.1)
#> crayon 1.5.0 2022-02-14 [1] CRAN (R 4.1.2)
#> DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.3)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2)
#> dplyr 1.0.8 2022-02-08 [1] CRAN (R 4.1.2)
#> ellipse 0.4.2 2020-05-27 [1] CRAN (R 4.1.2)
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#> ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.2)
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#> igraph 1.2.11 2022-01-04 [1] CRAN (R 4.1.2)
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#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
#> magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2)
#> MASS * 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
#> Matrix 1.3-4 2021-06-01 [2] CRAN (R 4.1.2)
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#> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
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#>
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#> [2] C:/Program Files/R/R-4.1.2patched/library
#>
#> ------------------------------------------------------------------------------
🤔 Expected behavior:
The perf() function is built to handle nzv features. Hence, it should ideally raise a warning to the fact that features have nzv, but should be able to proceed properly.
💡 Possible solution:
Error is occurring at line 542. Likely a result of Y.pred containing columns for every feature whereas Y.hat containing columns for all non-nzv features. Hence, adjusting this line to:
Ypred[omit, nzv.Y, h] = Y.hat[, , 1]
may solve the bug.
