Error of delete mode
Hi !
I have already downloaded the latest model, but I encountered an error when I tried to use "delete" mode to perturbate one gene, could you please help me fix this problem?
My codes are as below:
from geneformer import InSilicoPerturber
isp = InSilicoPerturber(perturb_type="delete",
perturb_rank_shift=None,
genes_to_perturb=["ENSG00000196843"],
combos=0,
anchor_gene=None,
model_type="CellClassifier",
num_classes=2,
emb_mode="cell_and_gene",
max_ncells=1000,
emb_layer=0,
forward_batch_size=256,
nproc=32)
isp.perturb_data("model",
"test.dataset",
"output catalog",
"output prefix")
And the errors be like:
Sincerely hope to obtain your answer, thank you !
Thank you for your interest in Geneformer! The error message indicates there are no cells with the gene you indicated. Since this model uses an updated dictionary, it would be good to ensure you tokenized your single cell RNAseq data with the new dictionary and that your in silico perturbation is using the new dictionary to convert the Ensembl ID you provide.
Thank you so much for your reply, Christina ! I will retry it as the advice you offered, by the way, could you please reply the question in discussion #391 which really bothers me for a lot of time ? thank you so so much again !