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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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Problem with `filter()` input `..1` #42

Open rahulnutron opened 3 years ago

rahulnutron commented 3 years ago

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 commented 3 years ago

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:

Best, Erica

rahulnutron commented 3 years ago

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’

rahulnutron commented 3 years ago

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

Thanks a lot, Regards, Rahul