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amc-heme / scExploreR

Shiny app for single cell omics data visualization
https://amc-heme.github.io/scExploreR/
MIT License
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Error when running differential expression #306

Closed jlbecker1 closed 1 month ago

jlbecker1 commented 4 months ago

Hello, When I attempt to run differential expression I receive an error related to the DGE table column names. I am working with a Seurat object saved as an .rds file (Seurat version 4.3.0). I am able to run differential expression using presto on it's own with the same Seurat object. I have no issue making any of the plots available, it's just the gene expression. The console shows: 2024-05-31 14:43:02.745038 [INFO] DGE Tab: Begin Presto [1] "DGE table colnanes" NULL Screen shot of app: image

wish1832 commented 4 months ago

Hi Jennifer,

Thanks for reaching out. Can you send me the text in the grey notification on the right of the screen? If possible, please include the beginning too, which likely got cut off. You may be able to get the full message by right-clicking on the notification text and selecting "select element" to open your browser's console.

I'll push an update to print this info in the console logs too, to make this process easier.

All the best,

Bill Showers

jlbecker1 commented 4 months ago

Hi Bill, Thank you for getting back to be so quickly. When I choose select element I am able to see the full error message. The first line is "Error: features must be one of "Xkr4", "Rp1 (long list of genes here)" and the last line is "not "data".." I'm able to make feature plots with no issue so I know that the gene names are there.

jlbecker1 commented 3 months ago

I just wanted to add an update that this happens to me when I use the triana_et_al_condensed data from your GitHub as well. Thanks again for your help.

wish1832 commented 2 months ago

Hi Jennifer,

Apologies for the delay in response. I attempted to re-create this with the triana_et_al_condensed data, and was unable to do so. Could you send me a screenshot of the Differential Expression tab with this object, showing the selections you made before pressing "Update"?

jlbecker1 commented 2 months ago

This is what I tried most recently

image
agillen commented 2 months ago

Can confirm that this is definitely Seurat 4.x.x-specific. Upgrading to Seurat 5.x.x will solve it, but recognize that might not be practical. We'll try to track down the underlying issue today.

wish1832 commented 2 months ago

This is linked to a programming issue in a dependency we manage, that causes the error you shared when using Seurat 4.x.x. amc-heme/scDE#6

agillen commented 1 month ago

Resolved with amc-heme/scDE#7.

@jlbecker1 - thanks so much for reporting this issue. Can you please confirm that reinstalling scDE from GitHub resolves this for you?

remotes::install_github("amc-heme/scDE")

wish1832 commented 1 month ago

And just in case updating scDE causes different issues, please try updating scExploreR, and contact us if that does not work.

remotes::install_github("amc-heme/scExploreR")

jlbecker1 commented 1 month ago

Yes, this worked. Thank you so much for your help!