Hi all,

I am trying to save my Seurat object to h5ad to use it as Anndata, I did it before using MuDataSeurat, with Seurat_4.3.0.1.

`seurat_object = CreateSeuratObject(counts = out, project = 'sample_name')

str(seurat_object)

1st str:

Formal class 'Seurat' [package "SeuratObject"] with 13 slots
  ..@ assays      :List of 1
  .. ..$ RNA:Formal class 'Assay' [package "SeuratObject"] with 8 slots
  .. .. .. ..@ counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:5253276] 14 29 38 91 115 124 137 156 197 226 ...
  .. .. .. .. .. ..@ p       : int [1:4587] 0 1412 2343 3385 4580 5000 5850 7137 8320 9391 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 20420 4586
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:20420] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ...
  .. .. .. .. .. .. ..$ : chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
  .. .. .. .. .. ..@ x       : num [1:5253276] 0.934 0.818 0.881 0.798 0.802 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:5253276] 14 29 38 91 115 124 137 156 197 226 ...
  .. .. .. .. .. ..@ p       : int [1:4587] 0 1412 2343 3385 4580 5000 5850 7137 8320 9391 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 20420 4586
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:20420] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ...
  .. .. .. .. .. .. ..$ : chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
  .. .. .. .. .. ..@ x       : num [1:5253276] 0.934 0.818 0.881 0.798 0.802 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ scale.data   : num[0 , 0 ] 
  .. .. .. ..@ key          : chr "rna_"
  .. .. .. ..@ assay.orig   : NULL
  .. .. .. ..@ var.features : logi(0) 
  .. .. .. ..@ meta.features:'data.frame':  20420 obs. of  0 variables
  .. .. .. ..@ misc         : list()
  ..@ meta.data   :'data.frame':    4586 obs. of  3 variables:
  .. ..$ orig.ident  : Factor w/ 1 level "CS23_F": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ nCount_RNA  : num [1:4586] 2192 1357 1536 1792 751 ...
  .. ..$ nFeature_RNA: int [1:4586] 1412 930 1040 1193 420 847 1287 1178 1066 651 ...
  ..@ active.assay: chr "RNA"
  ..@ active.ident: Factor w/ 1 level "CS23_F": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..- attr(*, "names")= chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
  ..@ graphs      : list()
  ..@ neighbors   : list()
  ..@ reductions  : list()
  ..@ images      : list()
  ..@ project.name: chr "CS23_F"
  ..@ misc        : list()
  ..@ version     :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 4 1 3
  ..@ commands    : list()
  ..@ tools       : list()
'Seurat' 

Then with MuDataSeurat::WriteH5AD(seurat_object, "path/seuratobject.h5ad")` I never had problem.

Now when I am using Seurat V5 I get this error with MuDataSeurat.

Error in (function (cl, name, valueClass)  : 
  ‘meta.features’ is not a slot in class “Seurat”

I checked the Seurat str and slots are different in the updated version, there is no meta.feature.

2nd str:

Formal class 'Seurat' [package "SeuratObject"] with 13 slots
  ..@ assays      :List of 1
  .. ..$ RNA:Formal class 'Assay5' [package "SeuratObject"] with 8 slots
  .. .. .. ..@ layers    :List of 1
  .. .. .. .. ..$ counts:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. .. ..@ i       : int [1:14994601] 154 240 493 541 546 567 624 675 684 693 ...
  .. .. .. .. .. .. ..@ p       : int [1:6975] 0 425 1244 1680 5294 7829 10590 13797 15113 15752 ...
  .. .. .. .. .. .. ..@ Dim     : int [1:2] 33538 6974
  .. .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. .. ..$ : NULL
  .. .. .. .. .. .. .. ..$ : NULL
  .. .. .. .. .. .. ..@ x       : num [1:14994601] 0.936 0.985 1.899 0.979 0.973 ...
  .. .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ cells     :Formal class 'LogMap' [package "SeuratObject"] with 1 slot
  .. .. .. .. .. ..@ .Data: logi [1:6974, 1] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. .. .. ..$ : chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ...
  .. .. .. .. .. .. .. ..$ : chr "counts"
  .. .. .. .. .. ..$ dim     : int [1:2] 6974 1
  .. .. .. .. .. ..$ dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ...
  .. .. .. .. .. .. ..$ : chr "counts"
  .. .. .. ..@ features  :Formal class 'LogMap' [package "SeuratObject"] with 1 slot
  .. .. .. .. .. ..@ .Data: logi [1:33538, 1] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. .. .. ..$ : chr [1:33538] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ...
  .. .. .. .. .. .. .. ..$ : chr "counts"
  .. .. .. .. .. ..$ dim     : int [1:2] 33538 1
  .. .. .. .. .. ..$ dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:33538] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ...
  .. .. .. .. .. .. ..$ : chr "counts"
  .. .. .. ..@ default   : int 1
  .. .. .. ..@ assay.orig: chr(0) 
  .. .. .. ..@ meta.data :'data.frame':   33538 obs. of  0 variables
  .. .. .. ..@ misc      :List of 1
  .. .. .. .. ..$ calcN: logi TRUE
  .. .. .. ..@ key       : chr "rna_"
  ..@ meta.data   :'data.frame':  6974 obs. of  3 variables:
  .. ..$ orig.ident  : Factor w/ 1 level "CS23LV": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ nCount_RNA  : num [1:6974] 746 1539 535 8631 5633 ...
  .. ..$ nFeature_RNA: int [1:6974] 425 818 435 3612 2532 2752 3179 1316 639 2267 ...
  ..@ active.assay: chr "RNA"
  ..@ active.ident: Factor w/ 1 level "CS23LV": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..- attr(*, "names")= chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ...
  ..@ graphs      : list()
  ..@ neighbors   : list()
  ..@ reductions  : list()
  ..@ images      : list()
  ..@ project.name: chr "CS23LV"
  ..@ misc        : list()
  ..@ version     :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 5 0 0
  ..@ commands    : list()
  ..@ tools       : list()

I tried to get the older version again, but I also get the second str of Seurat object each time.

Does anyone know how can I get the first str of Seurat object back or know another way to save it to h5ad?

Thanks