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Unable to run FindAllMarkers() #5441
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jctac, this is a bug with MAST in Seurat 4.0.6. See this issue: #5419 You can either use a previous version of Seurat, like 4.0.5, or a statistical test other than MAST. |
This should have been fixed in Feel free to reopen if there are followup issues. |
Thank you. MAST works with v4.0.5! |
Hello. I am using Seurat 5 and am facing this issue. I have integrated data, but I am using the RNA assay. Can you please assist? diffgenes.d1 <- FindAllMarkers(sets, assay="RNA", logfc.threshold = 0.4, test.use="negbinom", min.diff.pct=0.25, return.thresh=0.05) returns this error: |
is this solved? I got the same issue on Seurat5 |
I've tried Seurat v4.3.1 with different tests, but I still got the issue. |
Same here |
same here, not working both in R 4.3-x86_64, R-4.3-arm64 and R 4.2-arm64. Seurat v5 and Seurat v4.4.0. MAST and other tests gave me the same issue. Anyone who solve this issue? |
Anyone solved this issue? |
If you're okay with using MAST I was finding explicit definition of group.by and test.use to circumvent this error, e.g. |
I am still having this same problem with Seurat V5.0.1. |
same here |
same here - cannot run find all markers. Warning: No DE genes identified Not sure if this is a related issue, but I am also not able to rename identities; R version 4.3.2, Seurat_5.0.0 |
Just in case this could help. I realized that the active.ident should be assigned by Ident() instead of seurat.obj@active.ident <- if we want to change it manually. Then I solved this problem and calculated the markers. |
seurat v5.0.1 and R for 4.3.2 |
Yes! this worked for me too! thanks for sharing! |
I still don't know in which step to do this: |
in fact, you do not have to do this cause the active.ident would be assigned automatically when you run findcluster() function : )
…---Original---
From: ***@***.***>
Date: Sat, Jan 27, 2024 22:45 PM
To: ***@***.***>;
Cc: ***@***.******@***.***>;
Subject: Re: [satijalab/seurat] Unable to run FindAllMarkers() (Issue #5441)
I still don't know in which step to do this:
the active.ident should be assigned by Ident() instead of ***@***.***
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The default setting was to analyze the differential expressed genes(DEGs) in clusters, but i want to analyze the DEGs in my annoted celltypes. So i want to change the active.ident to the celltypes~ |
just after the findcluster() |
Not working and I am having the same issue |
Hi, |
Hello, I loaded the object before merging the metadata and the function worked fine again. I guess left_join function might work better. |
Hello, i know you may have many way to solve this problem.But, i also want to share the way that solves the trouble by "joinlaryers()" function.You can solves this wrong by running "object <- joinlaryers(object)" after using FindAllMarkers. |
Hi I recently was able to fix it by doing this: |
I experienced the same issue with Seurat 5.0.3 and R 4.3.3. I had several datasets, which then merged with merge() similar to @anayan321. The issue is solved by JoinLayers(). |
Hello,
I have been trying to run FindAllMarkers on an SCTransform'd dataset that has 6 clusters. Below is the error message I get in every R session I tried to run the code. However, I can run FindAllMarkers() on the pbmc3k dataset without any problems. I would really appreciate your help.
Thank you,
jctac
ERROR MESSAGE:
Calculating cluster 0
Done!
Calculating cluster 1
Done!
Calculating cluster 2
Done!
Calculating cluster 3
Done!
Calculating cluster 4
Done!
Calculating cluster 5
Done!
Warning: No DE genes identified
Warning: The following tests were not performed:
Warning: When testing 0 versus all:
$ operator is invalid for atomic vectors
Warning: When testing 1 versus all:
$ operator is invalid for atomic vectors
Warning: When testing 2 versus all:
$ operator is invalid for atomic vectors
Warning: When testing 3 versus all:
$ operator is invalid for atomic vectors
Warning: When testing 4 versus all:
$ operator is invalid for atomic vectors
Warning: When testing 5 versus all:
$ operator is invalid for atomic vectors
CODE:
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