Closed XiaoMi93 closed 2 weeks ago
As I only have scRNA-seq data, so I set the condition to ctrl for all cells during step 2 in the data_tutorial.ipynb file ((2) Create your own Perturb-Seq data). I got this error: AttributeError Traceback (most recent call last) Cell In[50], line 7 ----> 7 pert_data.new_data_process(dataset_name = scRNA', adata = adata) # specific dataset name and adata object
File [~/anaconda3/lib/python3.8/site-packages/gears/pertdata.py:250), in PertData.new_data_process(self, dataset_name, adata, skip_calc_de) 248 os.mkdir(save_data_folder) 249 self.dataset_path = save_data_folder --> 250 self.adata = get_DE_genes(adata, skip_calc_de) 251 if not skip_calc_de: 252 self.adata = get_dropout_non_zero_genes(self.adata)
File ~/anaconda3/envs/Tres/lib/python3.8/site-packages/gears/data_utils.py:64, in get_DE_genes(adata, skip_calc_de) 62 adata.obs = adata.obs.astype('category') 63 if not skip_calc_de: ---> 64 rank_genes_groups_by_cov(adata, 65 groupby='condition_name', 66 covariate='cell_type', 67 control_group='ctrl_1', 68 n_genes=len(adata.var), 69 key_added = 'rank_genes_groups_cov_all') ... 631 'pvals_adj': 'float64', 632 } 634 for col in test_obj.stats.columns.levels[0]:
AttributeError: 'NoneType' object has no attribute 'columns'
I think this is because I only provide one condition. Does this mean that I can not directly implement Gears on non-perturb-seq data?
Sorry for the delayed response!
It's hard to follow exactly which dataset you used for training but if I understand correctly you tried using non-perturb seq data to train GEARS. This will not work as GEARS needs perturbational data, ideally from a few different genetic perturbations.
If I misunderstood your question, please feel free to re-open this issue.
I too have the same question as @XiaoMi93!
I was wondering if one can use one of the pre-trained models (on Perturb-seq data) and apply them to scRNA-seq data to infer possible transcriptional response to a list of known/given perturbations; not to train the model per se but to apply the ones already trained on a different data source, despite them using different cell types and tissue just to inquire about possible similarities.
Thanks in advance!
Hi, Thank you for publishing such an excellent paper! I'm new to perturb-seq and only have single cell transcriptome data. I wonder whether I can use gears directly on the scRNA-seq data to infer the perturbation. Or I must provide my own perturb-seq data. Thanks!