MTXmodel 1.2.3
I was running the MTX model Demo
library(MTXmodel)
input_data <- read.table("HMP2_pwyRNA.tsv", sep="\t",header=T,row.names=1)
input_metadata <-read.table("HMP2_metadata.tsv", sep="\t",header=T,row.names=1)
input_dnadata <- read.table("HMP2_pwyDNA.tsv", sep="\t",header=T,row.names=1)
fit_data <- MTXmodel(
input_data, input_metadata, 'demo_output', transform = "LOG",
fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
random_effects = c('site', 'subject'),
reference = "diagnosis,nonIBD",
normalization = 'NONE',
standardize = FALSE,
input_dnadata = input_dnadata
)
leading to the following error:
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
My R session:
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Vienna
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] MTXmodel_1.2.3 sva_3.48.0
[3] BiocParallel_1.34.2 genefilter_1.82.1
[5] mgcv_1.8-42 nlme_3.1-162
[7] pheatmap_1.0.12 EnhancedVolcano_1.18.0
[9] DESeq2_1.40.2 SummarizedExperiment_1.30.2
[11] Biobase_2.60.0 MatrixGenerics_1.12.3
[13] matrixStats_1.0.0 GenomicRanges_1.52.0
[15] GenomeInfoDb_1.36.2 IRanges_2.34.1
[17] S4Vectors_0.38.1 BiocGenerics_0.46.0
[19] cowplot_1.1.1 Matrix_1.6-1
[21] gtable_0.3.4 ggrepel_0.9.3
[23] gridExtra_2.3 reshape_0.8.9
[25] PerformanceAnalytics_2.0.4 xts_0.13.1
[27] zoo_1.8-12 plotrix_3.8-2
[29] compare_0.2-6 fpc_2.2-10
[31] cluster_2.1.4 phangorn_2.11.1
[33] ade4_1.7-22 vegan_2.6-4
[35] lattice_0.21-8 permute_0.9-7
[37] GUniFrac_1.7 lubridate_1.9.2
[39] forcats_1.0.0 stringr_1.5.0
[41] dplyr_1.1.3 purrr_1.0.2
[43] readr_2.1.4 tidyr_1.3.0
[45] tibble_3.2.1 ggplot2_3.4.3
[47] tidyverse_2.0.0 phyloseq_1.44.0
[49] ape_5.7-1
loaded via a namespace (and not attached):
[1] splines_4.3.1 bitops_1.0-7 lpsymphony_1.28.1
[4] XML_3.99-0.14 rpart_4.1.19 lifecycle_1.0.3
[7] edgeR_3.42.4 vroom_1.6.3 prabclus_2.3-2
[10] MASS_7.3-60 magrittr_2.0.3 limma_3.56.2
[13] flexmix_2.3-19 DBI_1.1.3 RColorBrewer_1.1-3
[16] abind_1.4-5 zlibbioc_1.46.0 quadprog_1.5-8
[19] RCurl_1.98-1.12 hash_2.2.6.3 nnet_7.3-19
[22] GenomeInfoDbData_1.2.10 rmutil_1.1.10 spatial_7.3-16
[25] annotate_1.78.0 getopt_1.20.3 codetools_0.2-19
[28] DelayedArray_0.26.7 tidyselect_1.2.0 farver_2.1.1
[31] stable_1.1.6 jsonlite_1.8.7 multtest_2.56.0
[34] survival_3.5-5 iterators_1.0.14 foreach_1.5.2
[37] tools_4.3.1 Rcpp_1.0.11 glue_1.6.2
[40] withr_2.5.0 BiocManager_1.30.22 timeSeries_4031.107
[43] fastmap_1.1.1 rhdf5filters_1.12.1 fansi_1.0.4
[46] digest_0.6.33 timechange_0.2.0 R6_2.5.1
[49] colorspace_2.1-0 RSQLite_2.3.1 diptest_0.76-0
[52] modeest_2.4.0 utf8_1.2.3 generics_0.1.3
[55] data.table_1.14.8 robustbase_0.99-0 class_7.3-22
[58] httr_1.4.7 S4Arrays_1.0.5 pkgconfig_2.0.3
[61] timeDate_4022.108 modeltools_0.2-23 blob_1.2.4
[64] XVector_0.40.0 pcaPP_2.0-3 biomformat_1.28.0
[67] clue_0.3-64 logging_0.10-108 scales_1.2.1
[70] optparse_1.7.3 png_0.1-8 rstudioapi_0.15.0
[73] tzdb_0.4.0 reshape2_1.4.4 statip_0.2.3
[76] cachem_1.0.8 rhdf5_2.44.0 parallel_4.3.1
[79] AnnotationDbi_1.62.2 fBasics_4022.94 pillar_1.9.0
[82] vctrs_0.6.3 xtable_1.8-4 mvtnorm_1.2-3
[85] cli_3.6.1 locfit_1.5-9.8 compiler_4.3.1
[88] rlang_1.1.1 crayon_1.5.2 labeling_0.4.3
[91] mclust_6.0.0 plyr_1.8.8 stringi_1.7.12
[94] munsell_0.5.0 Biostrings_2.68.1 hms_1.1.3
[97] stabledist_0.7-1 bit64_4.0.5 Rhdf5lib_1.22.0
[100] KEGGREST_1.40.0 statmod_1.5.0 kernlab_0.9-32
[103] igraph_1.5.1 memoise_2.0.1 biglm_0.9-2.1
[106] fastmatch_1.1-4 DEoptimR_1.1-2 bit_4.0.5
This probably relates to:
Running the same dataset in Maaslin2 works without any problem.