Problem with `filter()` input `..1`

Question

Problem with `filter()` input `..1`

rahulnutron opened this issue 3 years ago · comments

Dear Authors,

Thanks for creating such a useful tool!

I am trying to use this tool with processed data from Seurat object. However, in the Improved_Seurat_Pre_Process I am getting an error. I will be grateful, if you could suggest what might went wrong.

regards,
Rahul

newFiles = Improved_Seurat_Pre_Process(sto_wt.dataset, num_genes=50, write_files=TRUE)

Error: Problem with filter() input ..1.
x object 'avg_logFC' not found
i Input ..1 is top_n_rank(num_genes, avg_logFC).
i The error occurred in group 1: cluster = "0".
Run rlang::last_error() to see where the error occurred.

EDePasquale · Answer 1 · Wed Dec 02 2020 00:19:49 GMT+0800 (China Standard Time)

Hi,

Are you using the version of DoubletDecon I updated yesterday or a previous version? I made an attempt to fix this problem that passed all of my testing, but it still might be broken in some cases.

Could you please send me the following:

Seurat version (packageVersion("Seurat"))
R version

Best,
Erica

Rahul Shaw · Answer 2 · Wed Dec 02 2020 00:24:42 GMT+0800 (China Standard Time)

Thank you for a quick reply!
I am using an old version of DoubletDecon, I need to update it to see if the problem exists on the newer version or not.
I will let you know.

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"

packageVersion("Seurat")
[1] ‘3.9.9.9010’

Rahul Shaw · Answer 3 · Wed Dec 02 2020 01:36:02 GMT+0800 (China Standard Time)

Dear Erica,
After the update, there is no error.

Thanks a lot,
Regards,
Rahul