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[Error] zero counts of overdispersed genes #83
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Hi Ji-Hye, Are you filtering cells with low counts (e.g. less than 200 or 500)? My suspicion is that those cells causing the problem may have overall low cell counts and you can avoid the issue by filtering cells with low counts first. And are you using the default of 2000 overdispersed genes? You could maybe try 3000 but I wouldn't go much higher than that because eventually it introduces a lot of noise when you normalize genes to uniform variance. I'll consider printing a full list of the offending cells in the future. |
Yes, I proceeded with the analysis using only the final remaining cells after removing those with fewer than 200 counts, and completing all additional processing and annotation steps. Even when attempting with 3000 genes, I encountered the same error with 12 cells. Thank you for the prompt response and assistance! |
Hi, I encountered the same errors! I would like to know if adjusting the number of variable genes would affect the results?Thanks! |
Hi, dylkot.
Thank you for developing the convenient tool.
I encountered the following error while trying to use your tool with an R script. It says to "Filter those cells and re-run or adjust the number of overdispersed genes."
However, I want to remove cells. The error message only mentions 5 cells, making it difficult to remove the remaining cells. Is there a way to remove them?
Additionally, I'm curious if increasing the number of high variable genes might be a better approach than removing cells. Which method would you recommend?
Thank you for your help!
Ji-Hye Choi
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