Comments (3)
davidhbrann
commented on June 3, 2024
I also just got the same error when using either FindMarkers or FindMarkersNode with "negbinom":
"FindMarkers"
Error in while ((it <- it + 1) < limit && abs(del) > eps) { :
missing value where TRUE/FALSE needed
Calls: FindMarkers ... lapply -> FUN -> summary -> glm.nb -> as.vector -> theta.ml
In addition: Warning message:
In [<-.data.frame(*tmp*, , "GENE", value = list(DS11TCCTTATTTCAG = 6L, :
provided 6207 variables to replace 1 variables
from seurat.
commented on June 3, 2024
If you could provide some sample data that recreates this error or the object itself, that would be helpful. Can't seem to reproduce it on the datasets I have.
from seurat.
andrewwbutler
commented on June 3, 2024
Resolved the bug. Reinstalling should allow you to run any of the marker detection functions with the "negbinom" test without problems.
from seurat.
Related Issues (20)
- Why are the points in the plots drawn by the SpatialFeaturePlot() function very small? HOT 3
- Problems with RunPCA when npcs > 25 HOT 2
- "The following N features requested have not been scaled" warning after running SCTransform
- NormalizeData() FindVariableFeatures() ScaleData() RunPCA() extremely slow with large dataset (1M+ cell 100+ samples). HOT 1
- SCTransform fails with error: no applicable method for 'as.sparse' applied to an object of class "c('double', 'numeric')"
- Combining counts of 2 genes into 1 gene - spatial
- SCTransform in a merged and subsetted object how to set variable features
- Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length HOT 2
- Integrating multiple objects with IntegrateEmbeddings() erases all previous reductions
- PseudobulkExpressoin vs AggregateExpression HOT 2
- How to deal with technical replicates of scRNAseq data? HOT 1
- Error in running IntegrateData()
- DoHeatmap donot return plot HOT 1
- MapQuery for CITE-seq, using a CITE-seq reference
- Warning: Adding a dimensional reduction (integrated.rpca) without the associated assay being present
- Can't convert from Seurat to anndata
- Visium image shrunk HOT 2
- RCTD for Xenium data
- remotes::install_github("satijalab/seurat-data", quiet = TRUE) does not work HOT 2
- Error in validObject(.Object) : invalid class "ScaledMatrix" object: the supplied seed must support extract_array()
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from seurat.