Raw Data not Present in Loom File

[iSinedeus]

Hello,

I am trying to convert a seurat object into a loom file to be opened in python using scanpy. I have been able to create the loom file but I run into an error using scanpy when I try to normalize the data that I believe indicates the raw data is not present in the file. Is the raw data referred to by scanpy not present by default if you create a loom file from a normalized seurat object? The error I receive in python is: noneType object has no attribute X after running the code: adata2 = sc.AnnData(X=adata.raw.X, r=adata.raw.var, obs = adata.obs).

I tried to create a loom file using the "RNA" assay but I get the following error:
rcc_crc_36s.loom <- as.loom(rcc_crc_36s, filename = "rcc_crc_36s_RNA2.loom", verbose = FALSE, assay = "RNA")
Transposing input data: loom file will show input columns (cells) as rows and input rows (features) as columns
This is to maintain compatibility with other loom tools
Adding: CellID
Adding: Gene
Error in attributes[[i]] : subscript out of bounds

I have received this error message previously and based on Issue #36 I have used the findvariablefeatures function to correct this but this appears not to work in this case when I'm attempting to create a file from the "RNA" assay. I can create a loom file from this exact object if I do not specify using the "RNA" assay. Or would it be correct to normalize my dataset on an individual sample basis similar to the sctransform workflow for integration and just save that dataset and not use the normalization steps in scanpy? I'm a bit new to using loom so I appreciate any advice you're able to offer.

Thank you