Open mdurante1 opened 5 years ago
Hi Michael,
Thanks for trying the tool. It looks like a pandas data frame issue, and one gene in your matrix is causing the problem. Can you remove the genes that are lowly expressed, say, the average nUMI is less than 0.1 and try the tool again? And if you can remove the "NA" in your input matrix, that will be helpful, too.
Best, Feiyang
Hi, I append to stumbled upon the same issue a couple of days ago. It arose from a duplicate gene in the training dataset (C2ORF15). After removing this gene from the common_gene array. Everything worked smoothly.
Edit: It also append with another dataset and C2ORF15 was the culprit as well. This gene doesn't seem to be duplicated in the input dataset although it is clearly duplicated in sets[0]. This is why scale_sets([train_set, test_set]) function fails to execute properly.
Hope that helps Best Raphael
I have the same problem. Turns out there is indeed C2ORF15 duplicate in the training dataset....
Hi All,
Thanks for bringing the problem up. I revised the code to remove the duplicated genes in the datasets. Now we won't get the shape error from pandas dataframe.
Best, Feiyang
Hello,
I have tested your tool out on the example data that you provided and it seems to work very nicely. I proceeded to run my own data set with the default training set and received good results. I then tried to test the "tcell_subtype" dataset you describe in your manuscript and received the error below. Can you please provide any insight into the source of this error?
Best, Michael