I am unable to reproduce the error here. I receive the following results:
suppressMessages(library(mixOmics))
data(breast.TCGA)
train.samples <- c(1:6, 77:83)
X.train <- breast.TCGA$data.train$mirna[train.samples, ]
Y.train <- as.vector(breast.TCGA$data.train$subtype[train.samples])
test.samples <- c(7,8, 84, 85)
X.test <- breast.TCGA$data.train$mirna[test.samples, ]
Y.test <- as.vector(breast.TCGA$data.train$subtype[test.samples])
MyResult.splsda.final <- splsda(X.train, Y.train,
keepX = c(100,100)) # tried a range of values
# USING TRAINING DATA
pred=predict(MyResult.splsda.final, X.train)
Prediction <- pred$class$mahalanobis.dist[, 1]
Prediction
#> A0FJ A13E A0G0 A0SX A143 A0DA A0B0 A18S A0CS A0EI
#> "Basal" "Basal" "Basal" "Basal" "Basal" "Basal" "LumA" "LumA" "LumA" "LumA"
#> A0IO A0T6 A1AU
#> "LumA" "LumA" "LumA"
# USING TESTING DATA
pred=predict(MyResult.splsda.final, X.test)
Prediction <- pred$class$mahalanobis.dist[, 1]
Prediction
#> A0B3 A0I2 A07Z A0XS
#> "LumA" "Basal" "LumA" "LumA"
Created on 2022-09-20 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 19044)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz Australia/Sydney
#> date 2022-09-20
#> pandoc 2.18 @ D:/Programs/Work Programs/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
#> BiocParallel 1.30.3 2022-06-07 [1] Bioconductor
#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.1)
#> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1)
#> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
#> corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.2.0)
#> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
#> dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.1)
#> ellipse 0.4.3 2022-05-31 [1] CRAN (R 4.2.1)
#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
#> ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.1)
#> ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.2.1)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.1)
#> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> igraph 1.3.4 2022-07-19 [1] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lattice * 0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> MASS * 7.3-58.1 2022-08-03 [1] CRAN (R 4.2.1)
#> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.1)
#> matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.1)
#> mixOmics * 6.20.0 2022-04-26 [1] Bioconductor (R 4.2.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
#> plyr 1.8.7 2022-03-24 [1] CRAN (R 4.2.1)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.1)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
#> rARPACK 0.11-0 2016-03-10 [1] CRAN (R 4.2.1)
#> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
#> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.2.1)
#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1)
#> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.1)
#> RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.2.1)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.1)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
#> tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.1)
#> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.1)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.1)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
#>
#> [1] D:/Programs/Work Programs/R-4.2.1/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
To help I’d first need a reproducible example (as described here and in the banner). From there, we can potentially discuss me accessing your data and scripts to evaluate them for issues. Feel free to directly message me via the forum