scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
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Madiha • 0
@540419f7
Last seen 8 weeks ago
Pakistan

Hi,

New in scRNA-seq data analysis, having error "'RS4' object has no attribute 'T'" in fastMNN R function. I am not sure if there is something wrong with the data or this fastMNN function.

Any help would be highly appreciated!

Thanks,

Madiha

scanpy scRNAseq fastmnn r • 238 views
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Hello Madiha ... you'll have to provide considerable detail before we would be able to provide help. What is the exact error message? Try to grab the error text and paste it into the support site message box as "code". Also please provide results of sessionInfo() and any details about the command attempted and the data that were input. Thank you

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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

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I have resolved the issue, the problem with the data structure holding my data. Thanks!

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