Apologies in advance if this turns out to be a silly error... But I can't seem to solve it. Really appreciate some help if possible!
I'm new to this package, and I'm trying to run form_tensor on my seurat object.
I first created a project container as described in the walkthrough.
pbmc_container <- make_new_container(seurat_obj = Seurat_Obj, params=param_list, label_donor_sex = TRUE)
Then I tried form_tensor without changing any of the parameters
pbmc_container <- form_tensor(pbmc_container, donor_min_cells=5,
norm_method='trim', scale_factor=10000,
vargenes_method='norm_var_pvals', vargenes_thresh=.1,
scale_var = TRUE, var_scale_power = 2)
And I keep getting this error at the cleaning data step:
parsing data matrix by cell/tissue type...
cleaning data...
Error in count_data[, which(metadata$donors %in% donors_use)] :
incorrect number of dimensions
I have about 140 samples which I labelled as donors, and about 170 cell types. Some donors have less than 5 cells in a cell type, but all of them have more than 5 cells in total. I've tried changing the dataframe from factor to character, but it doesn't work. Any tips would be much appreciated!
Thank you!
Samuel
PS: I am able to run the code fine using your example data, so I'm not sure what the issue is with my own
Hi!
Apologies in advance if this turns out to be a silly error... But I can't seem to solve it. Really appreciate some help if possible!
I'm new to this package, and I'm trying to run form_tensor on my seurat object.
I first created a project container as described in the walkthrough. pbmc_container <- make_new_container(seurat_obj = Seurat_Obj, params=param_list, label_donor_sex = TRUE)
Then I tried form_tensor without changing any of the parameters pbmc_container <- form_tensor(pbmc_container, donor_min_cells=5, norm_method='trim', scale_factor=10000, vargenes_method='norm_var_pvals', vargenes_thresh=.1, scale_var = TRUE, var_scale_power = 2)
And I keep getting this error at the cleaning data step: parsing data matrix by cell/tissue type... cleaning data... Error in count_data[, which(metadata$donors %in% donors_use)] : incorrect number of dimensions
I have about 140 samples which I labelled as donors, and about 170 cell types. Some donors have less than 5 cells in a cell type, but all of them have more than 5 cells in total. I've tried changing the dataframe from factor to character, but it doesn't work. Any tips would be much appreciated!
Thank you!
Samuel
PS: I am able to run the code fine using your example data, so I'm not sure what the issue is with my own