Rounding of PICRUST2 table couts?

[marwa38]

I am getting an error when running your tutorial as shown in the below codes

> daa_results_df <- pathway_daa(abundance = kegg_abundance, 
+                               metadata = metadata, 
+                               group = "Region_Regime", 
+                               daa_method = "ALDEx2", select = NULL, reference = NULL)
Using column 'sample.ID' as sample identifier
Running ALDEx2 analysis...
Running ALDEx2 with multiple groups. This might take some time...

Error in Math.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  : 
  ‘round’ not meaningful for factors

Expected Behavior
I think that might be happening becasue the picrust2 tables counts need to be integers? based on the error / advice
https://forum.qiime2.org/t/aldex2-error-when-processing-picrust2-output/14104
I rounded and it is still not working giving the same error!
`kegg_abundance[, -1] <- round(kegg_abundance[, -1])

sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Europe/Paris
tzcode source: internal

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

other attached packages:
[1] patchwork_1.3.0 ggprism_1.0.5 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[6] dplyr_1.1.4 purrr_1.0.2 tidyr_1.3.1 ggplot2_3.5.1 tidyverse_2.0.0
[11] tibble_3.2.1 ggpicrust2_1.7.4 readr_2.1.5

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 fastmap_1.2.0
[4] ALDEx2_1.38.0 digest_0.6.37 NADA_1.6-1.1
[7] timechange_0.3.0 lifecycle_1.0.4 survival_3.8-3
[10] magrittr_2.0.3 compiler_4.4.2 rlang_1.1.4
[13] tools_4.4.2 yaml_2.3.10 knitr_1.49
[16] S4Arrays_1.6.0 interp_1.1-6 bit_4.5.0.1
[19] DelayedArray_0.32.0 RColorBrewer_1.1-3 aplot_0.2.4
[22] abind_1.4-8 BiocParallel_1.40.0 withr_3.0.2
[25] BiocGenerics_0.52.0 grid_4.4.2 ggh4x_0.3.0
[28] stats4_4.4.2 latticeExtra_0.6-30 colorspace_2.1-1
[31] scales_1.3.0 MASS_7.3-64 SummarizedExperiment_1.36.0
[34] cli_3.6.3 rmarkdown_2.29 crayon_1.5.3
[37] generics_0.1.3 RcppParallel_5.1.9 rstudioapi_0.17.1
[40] httr_1.4.7 tzdb_0.4.0 directlabels_2024.1.21
[43] zlibbioc_1.52.0 zCompositions_1.5.0-4 splines_4.4.2
[46] parallel_4.4.2 ggplotify_0.1.2 XVector_0.46.0
[49] matrixStats_1.5.0 yulab.utils_0.1.9 vctrs_0.6.5
[52] Matrix_1.7-1 jsonlite_1.8.9 gridGraphics_0.5-1
[55] IRanges_2.40.1 hms_1.1.3 S4Vectors_0.44.0
[58] bit64_4.5.2 jpeg_0.1-10 glue_1.8.0
[61] codetools_0.2-20 stringi_1.8.4 gtable_0.3.6
[64] deldir_2.0-4 GenomeInfoDb_1.42.1 quadprog_1.5-8
[67] GenomicRanges_1.58.0 UCSC.utils_1.2.0 RcppZiggurat_0.1.6
[70] munsell_0.5.1 pillar_1.10.1 htmltools_0.5.8.1
[73] truncnorm_1.0-9 GenomeInfoDbData_1.2.13 R6_2.5.1
[76] vroom_1.6.5 evaluate_1.0.1 lattice_0.22-6
[79] Biobase_2.66.0 png_0.1-8 Rfast_2.1.3
[82] ggfun_0.1.8 Rcpp_1.0.13-1 SparseArray_1.6.0
[85] xfun_0.49 fs_1.6.5 MatrixGenerics_1.18.0
[88] pkgconfig_2.0.3 `

[marwa38]

ALDEx2 v.1.28 worked!