Hi, thanks for the reply Vincent. here are my commands:

  'set.seed(55063)

  mob <- modelGeneVar(m_s, block = colData(m_s)$Sample)

  hmb <- getTopHVGs(mob, prop = 0.1)

  set.seed(55063)

  m_s_c<- fastMNN(m_s, subset.row = hmb, batch=m_s$Sample)'

and the error i got at fastmnn step: JNB highlight this line

  assays = [mat_converter.rpy2py(assay).T for assay in (se.assay(obj, n) for n in assay_names)] 

and the error is

 AttributeError: 'RS4' object has no attribute 'T'

And session info

 R version 4.2.1 (2022-06-23)
 Platform: x86_64-apple-darwin17.0 (64-bit)
 Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:

[1] C/UTF-8/C/C/C/C

attached base packages: [1] grid stats4 tools stats graphics grDevices utils
[8] datasets methods base

other attached packages: [1] MatrixEQTL_2.3 forcats_0.5.1
[3] stringr_1.4.0 purrr_0.3.4
[5] readr_2.1.2 tidyr_1.2.0
[7] tibble_3.1.8 tidyverse_1.3.2
[9] dplyr_1.0.9 circlize_0.4.15
[11] ComplexHeatmap_2.12.1 batchelor_1.12.3
[13] DropletUtils_1.16.0 scater_1.24.0
[15] ggplot2_3.3.6 scran_1.24.0
[17] scuttle_1.6.2 SingleCellExperiment_1.18.0 [19] SummarizedExperiment_1.26.1 Biobase_2.56.0
[21] GenomicRanges_1.48.0 GenomeInfoDb_1.32.3
[23] IRanges_2.30.0 S4Vectors_0.34.0
[25] BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[27] matrixStats_0.62.0 Matrix_1.4-1

loaded via a namespace (and not attached): [1] Rtsne_0.16 googledrive_2.0.0
[3] ggbeeswarm_0.6.0 colorspace_2.0-3
[5] rjson_0.2.21 ellipsis_0.3.2
[7] bluster_1.6.0 XVector_0.36.0
[9] GlobalOptions_0.1.2 BiocNeighbors_1.14.0
[11] fs_1.5.2 clue_0.3-61
[13] ggrepel_0.9.1 lubridate_1.8.0
[15] fansi_1.0.3 xml2_1.3.3
[17] codetools_0.2-18 R.methodsS3_1.8.2
[19] sparseMatrixStats_1.8.0 doParallel_1.0.17
[21] jsonlite_1.8.0 ResidualMatrix_1.6.0
[23] broom_1.0.0 cluster_2.1.3
[25] dbplyr_2.2.1 png_0.1-7
[27] R.oo_1.25.0 HDF5Array_1.24.2
[29] httr_1.4.3 compiler_4.2.1
[31] dqrng_0.3.0 backports_1.4.1
[33] assertthat_0.2.1 gargle_1.2.0
[35] limma_3.52.2 cli_3.3.0
[37] BiocSingular_1.12.0 rsvd_1.0.5
[39] igraph_1.3.4 gtable_0.3.0
[41] glue_1.6.2 GenomeInfoDbData_1.2.8
[43] Rcpp_1.0.9 cellranger_1.1.0
[45] vctrs_0.4.1 rhdf5filters_1.8.0
[47] iterators_1.0.14 DelayedMatrixStats_1.18.0 [49] rvest_1.0.2 beachmat_2.12.0
[51] lifecycle_1.0.1 irlba_2.3.5
[53] statmod_1.4.37 googlesheets4_1.0.1
[55] edgeR_3.38.4 zlibbioc_1.42.0
[57] scales_1.2.0 hms_1.1.1
[59] parallel_4.2.1 rhdf5_2.40.0
[61] RColorBrewer_1.1-3 gridExtra_2.3
[63] stringi_1.7.8 foreach_1.5.2
[65] ScaledMatrix_1.4.0 BiocParallel_1.30.3
[67] shape_1.4.6 rlang_1.0.4
[69] pkgconfig_2.0.3 bitops_1.0-7
[71] lattice_0.20-45 Rhdf5lib_1.18.2
[73] tidyselect_1.1.2 magrittr_2.0.3
[75] R6_2.5.1 generics_0.1.3
[77] metapod_1.4.0 DelayedArray_0.22.0
[79] DBI_1.1.3 pillar_1.8.0
[81] haven_2.5.0 withr_2.5.0
[83] RCurl_1.98-1.8 modelr_0.1.8
[85] crayon_1.5.1 utf8_1.2.2
[87] tzdb_0.3.0 viridis_0.6.2
[89] GetoptLong_1.0.5 readxl_1.4.0
[91] locfit_1.5-9.6 reprex_2.0.1
[93] digest_0.6.29 R.utils_2.12.0
[95] munsell_0.5.0 beeswarm_0.4.0
[97] viridisLite_0.4.0 vipor_0.4.5

please let me know if there is anything wrong