Hi,

I have a following Seurat obj ;

> str([email protected])
List of 4
 $ RNA      :Formal class 'Assay' [package "Seurat"] with 8 slots
  .. [email protected] counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:24330253] 25 30 32 42 43 44 51 59 60 62 ...
  .. .. .. [email protected] p       : int [1:10195] 0 4803 7036 11360 11703 15846 18178 20413 22584 27802 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:24330253] 1 2 1 1 1 3 1 1 1 1 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:24330253] 25 30 32 42 43 44 51 59 60 62 ...
  .. .. .. [email protected] p       : int [1:10195] 0 4803 7036 11360 11703 15846 18178 20413 22584 27802 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:24330253] 0.367 0.634 0.367 0.367 0.367 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] scale.data   : num [1:2000, 1:10194] -0.0829 -0.2648 -0.195 -0.0133 1.2823 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:2000] "PLEKHN1" "HES4" "ISG15" "LINC01342" ...
  .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. [email protected] key          : chr "rna_"
  .. [email protected] assay.orig   : NULL
  .. [email protected] var.features : chr [1:2000] "PTGDS" "IGLC3" "PPBP" "CXCL10" ...
  .. [email protected] meta.features:'data.frame':    36601 obs. of  5 variables:
  .. .. ..$ vst.mean                 : num [1:36601] 0 0 0 0.00392 0 ...
  .. .. ..$ vst.variance             : num [1:36601] 0 0 0 0.00391 0 ...
  .. .. ..$ vst.variance.expected    : num [1:36601] 0 0 0 0.00452 0 ...
  .. .. ..$ vst.variance.standardized: num [1:36601] 0 0 0 0.865 0 ...
  .. .. ..$ vst.variable             : logi [1:36601] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. [email protected] misc         : NULL
 $ unspliced:Formal class 'Assay' [package "Seurat"] with 8 slots
  .. [email protected] counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:20057627] 8 46 53 69 70 71 72 73 84 89 ...
  .. .. .. [email protected] p       : int [1:10195] 0 3837 6398 9489 10407 14220 16595 18856 20831 24609 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "BX004987.1" "AC145212.1" "MAFIP" "AC011043.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:20057627] 1 3 1 1 2 1 1 9 1 1 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:20057627] 8 46 53 69 70 71 72 73 84 89 ...
  .. .. .. [email protected] p       : int [1:10195] 0 3837 6398 9489 10407 14220 16595 18856 20831 24609 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "BX004987.1" "AC145212.1" "MAFIP" "AC011043.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:20057627] 1 3 1 1 2 1 1 9 1 1 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] scale.data   : num[0 , 0 ] 
  .. [email protected] key          : chr "unspliced_"
  .. [email protected] assay.orig   : NULL
  .. [email protected] var.features : logi(0) 
  .. [email protected] meta.features:'data.frame':    36601 obs. of  0 variables
  .. [email protected] misc         : NULL
 $ spliced  :Formal class 'Assay' [package "Seurat"] with 8 slots
  .. [email protected] counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:19059316] 48 49 50 54 59 60 61 65 70 72 ...
  .. .. .. [email protected] p       : int [1:10195] 0 3840 5465 8968 9150 12398 14145 15854 17504 21746 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "BX004987.1" "AC145212.1" "MAFIP" "AC011043.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:19059316] 1 1 3 1 1 1 1 1 1 2 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:19059316] 48 49 50 54 59 60 61 65 70 72 ...
  .. .. .. [email protected] p       : int [1:10195] 0 3840 5465 8968 9150 12398 14145 15854 17504 21746 ...
  .. .. .. [email protected] Dim     : int [1:2] 36601 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:36601] "BX004987.1" "AC145212.1" "MAFIP" "AC011043.1" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:19059316] 1 1 3 1 1 1 1 1 1 2 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] scale.data   : num[0 , 0 ] 
  .. [email protected] key          : chr "spliced_"
  .. [email protected] assay.orig   : NULL
  .. [email protected] var.features : logi(0) 
  .. [email protected] meta.features:'data.frame':    36601 obs. of  0 variables
  .. [email protected] misc         : NULL
 $ SCT      :Formal class 'Assay' [package "Seurat"] with 8 slots
  .. [email protected] counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:22836556] 12 17 21 22 23 45 59 60 74 79 ...
  .. .. .. [email protected] p       : int [1:10195] 0 2675 4907 7438 8739 12423 14750 16985 19156 21564 ...
  .. .. .. [email protected] Dim     : int [1:2] 20666 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:20666] "AL627309.1" "AL627309.5" "AL627309.4" "AL669831.2" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:22836556] 1 1 1 1 1 1 1 2 1 1 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. [email protected] i       : int [1:22836556] 12 17 21 22 23 45 59 60 74 79 ...
  .. .. .. [email protected] p       : int [1:10195] 0 2675 4907 7438 8739 12423 14750 16985 19156 21564 ...
  .. .. .. [email protected] Dim     : int [1:2] 20666 10194
  .. .. .. [email protected] Dimnames:List of 2
  .. .. .. .. ..$ : chr [1:20666] "AL627309.1" "AL627309.5" "AL627309.4" "AL669831.2" ...
  .. .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. .. .. [email protected] x       : num [1:22836556] 0.693 0.693 0.693 0.693 0.693 ...
  .. .. .. [email protected] factors : list()
  .. [email protected] scale.data   : num [1:3000, 1:10194] -0.1333 -0.5897 -1.0906 -0.0483 -0.0499 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:3000] "PLEKHN1" "HES4" "ISG15" "AL390719.3" ...
  .. .. .. ..$ : chr [1:10194] "AAACCCACATAACTCG-1" "AAACCCACATGTAACC-1" "AAACCCAGTGAGTCAG-1" "AAACCCAGTGCTTATG-1" ...
  .. [email protected] key          : chr "sct_"
  .. [email protected] assay.orig   : NULL
  .. [email protected] var.features : chr [1:3000] "GNLY" "IGKC" "S100A9" "S100A8" ...
  .. [email protected] meta.features:'data.frame':    20666 obs. of  6 variables:
  .. .. ..$ sct.detection_rate   : num [1:20666] 0.003924 0.051893 0.001177 0.000687 0.067393 ...
  .. .. ..$ sct.gmean            : num [1:20666] 0.002724 0.038556 0.000816 0.000476 0.050365 ...
  .. .. ..$ sct.variance         : num [1:20666] 0.003909 0.064675 0.001176 0.000686 0.081901 ...
  .. .. ..$ sct.residual_mean    : num [1:20666] -0.00392 -0.01045 0.0048 -0.00904 -0.00616 ...
  .. .. ..$ sct.residual_variance: num [1:20666] 0.779 0.894 1.275 0.75 0.965 ...
  .. .. ..$ sct.variable         : logi [1:20666] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. [email protected] misc         :List of 2
  .. .. ..$ vst.out  :List of 12
  .. .. .. ..$ model_str            : chr "y ~ log_umi"
  .. .. .. ..$ model_pars           : num [1:2000, 1:3] 0.137 14.691 2.243 2.874 0.746 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:2000] "B9D1" "XRCC5" "RPS12" "RPS3A" ...
  .. .. .. .. .. ..$ : chr [1:3] "theta" "(Intercept)" "log_umi"
  .. .. .. ..$ model_pars_outliers  : logi [1:2000] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. ..$ model_pars_fit       : num [1:20666, 1:3] 0.0475 0.4904 0.0527 0.0326 0.6443 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20666] "AL627309.1" "AL627309.5" "AL627309.4" "AL669831.2" ...
  .. .. .. .. .. ..$ : chr [1:3] "theta" "(Intercept)" "log_umi"
  .. .. .. .. ..- attr(*, "outliers")= logi [1:2000] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. ..$ model_str_nonreg     : chr ""
  .. .. .. ..$ model_pars_nonreg    : NULL
  .. .. .. ..$ arguments            :List of 24
  .. .. .. .. ..$ latent_var          : chr "log_umi"
  .. .. .. .. ..$ batch_var           : NULL
  .. .. .. .. ..$ latent_var_nonreg   : NULL
  .. .. .. .. ..$ n_genes             : num 2000
  .. .. .. .. ..$ n_cells             : num 5000
  .. .. .. .. ..$ method              : chr "poisson"
  .. .. .. .. ..$ do_regularize       : logi TRUE
  .. .. .. .. ..$ theta_regularization: chr "od_factor"
  .. .. .. .. ..$ res_clip_range      : num [1:2] -101 101
  .. .. .. .. ..$ bin_size            : num 500
  .. .. .. .. ..$ min_cells           : num 5
  .. .. .. .. ..$ residual_type       : chr "pearson"
  .. .. .. .. ..$ return_cell_attr    : logi TRUE
  .. .. .. .. ..$ return_gene_attr    : logi TRUE
  .. .. .. .. ..$ return_corrected_umi: logi TRUE
  .. .. .. .. ..$ min_variance        : num -Inf
  .. .. .. .. ..$ bw_adjust           : num 3
  .. .. .. .. ..$ gmean_eps           : num 1
  .. .. .. .. ..$ theta_estimation_fun: chr "theta.ml"
  .. .. .. .. ..$ theta_given         : NULL
  .. .. .. .. ..$ verbosity           : num 2
  .. .. .. .. ..$ verbose             : NULL
  .. .. .. .. ..$ show_progress       : NULL
  .. .. .. .. ..$ sct.clip.range      : num [1:2] -18.4 18.4
  .. .. .. ..$ genes_log_gmean_step1: Named num [1:2000] -2.4848 0.0795 1.6421 1.4171 -0.0858 ...
  .. .. .. .. ..- attr(*, "names")= chr [1:2000] "B9D1" "XRCC5" "RPS12" "RPS3A" ...
  .. .. .. ..$ cells_step1          : chr [1:5000] "CATGAGTTCGCGTCGA-1" "TCGCAGGCAGTCGTTA-1" "TCGTGCTAGGTTAAAC-1" "TTTGATCTCTCGCTTG-1" ...
  .. .. .. ..$ cell_attr            :'data.frame':  10194 obs. of  10 variables:
  .. .. .. .. ..$ orig.ident        : Factor w/ 1 level "10x10kPBMCdualIndex": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ nCount_RNA        : num [1:10194] 22575 7758 21733 860 15311 ...
  .. .. .. .. ..$ nFeature_RNA      : int [1:10194] 4803 2233 4324 343 4143 2332 2235 2171 5218 3199 ...
  .. .. .. .. ..$ nCount_spliced    : num [1:10194] 15555 4838 14972 225 9914 ...
  .. .. .. .. ..$ nFeature_spliced  : int [1:10194] 3840 1625 3503 182 3248 1747 1709 1650 4242 2502 ...
  .. .. .. .. ..$ nCount_unspliced  : num [1:10194] 12648 7323 10260 1509 12001 ...
  .. .. .. .. ..$ nFeature_unspliced: int [1:10194] 3837 2561 3091 918 3813 2375 2261 1975 3778 2856 ...
  .. .. .. .. ..$ percent.mt        : num [1:10194] 5.33 8.84 6.32 31.51 7.91 ...
  .. .. .. .. ..$ umi               : num [1:10194] 22575 7758 21733 860 15311 ...
  .. .. .. .. ..$ log_umi           : num [1:10194] 4.35 3.89 4.34 2.93 4.19 ...
  .. .. .. ..$ gene_attr            :'data.frame':  20666 obs. of  5 variables:
  .. .. .. .. ..$ detection_rate   : num [1:20666] 0.003924 0.051893 0.001177 0.000687 0.067393 ...
  .. .. .. .. ..$ gmean            : num [1:20666] 0.002724 0.038556 0.000816 0.000476 0.050365 ...
  .. .. .. .. ..$ variance         : num [1:20666] 0.003909 0.064675 0.001176 0.000686 0.081901 ...
  .. .. .. .. ..$ residual_mean    : num [1:20666] -0.00392 -0.01045 0.0048 -0.00904 -0.00616 ...
  .. .. .. .. ..$ residual_variance: num [1:20666] 0.779 0.894 1.275 0.75 0.965 ...
  .. .. .. ..$ times                :List of 7
  .. .. .. .. ..$ start_time    : POSIXct[1:1], format: "2020-12-12 19:54:11"
  .. .. .. .. ..$ get_model_pars: POSIXct[1:1], format: "2020-12-12 19:54:15"
  .. .. .. .. ..$ reg_model_pars: POSIXct[1:1], format: "2020-12-12 19:54:47"
  .. .. .. .. ..$ get_residuals : POSIXct[1:1], format: "2020-12-12 19:54:47"
  .. .. .. .. ..$ correct_umi   : POSIXct[1:1], format: "2020-12-12 19:54:58"
  .. .. .. .. ..$ get_gene_attr : POSIXct[1:1], format: "2020-12-12 19:55:11"
  .. .. .. .. ..$ done          : POSIXct[1:1], format: "2020-12-12 19:55:15"
  .. .. ..$ umi.assay: chr "RNA"

I converted this Seurat obj to Anndata by sceasy as follows;

> convertFormat(pbmc10k, from = "seurat", to="anndata", outFile = "pbmc10k.h5ad")
... storing 'Phase' as categorical
... storing 'hpca.fine' as categorical
... storing 'hpca.main' as categorical
... storing 'monaco.main' as categorical
... storing 'monaco.fine' as categorical
AnnData object with n_obs × n_vars = 10194 × 36601
    obs: 'nCount_RNA', 'nFeature_RNA', 'nCount_spliced', 'nFeature_spliced', 'nCount_unspliced', 'nFeature_unspliced', 'percent.mt', 'nCount_SCT', 'nFeature_SCT', 'SCT_snn_res.0.8', 'seurat_clusters', 'S.Score', 'G2M.Score', 'Phase', 'old.ident', 'hpca.fine', 'hpca.main', 'monaco.main', 'monaco.fine'
    var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable'
    obsm: 'X_pca', 'X_umap'
Warning message:
In .regularise_df([email protected], drop_single_values = drop_single_values) :
  Dropping single category variables:orig.ident

As you can see, for some reasons, the conversion did not pick up $spliced and $unspliced as vars but instead, it picked $[email protected] as vars. I would appreciate any explanation for this and any pointers to fix this.

Thanks.



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