Comments (2)
I figured out that I might be having trouble at this step: scaleNotCenterFast(t([email protected][[i]][[email protected], ]))
, so I modified the code: scale(t([email protected][[i]][[email protected], ]), center = FALSE, scale = TRUE)
. This allowed the function to run successfully.
I have two questions:
- What specific operations does scaleNotCenterFast() perform? This will help me better understand if my modification is appropriate.
- Is directly using scale() a feasible workaround here? Or do you recommend any other solutions?
from liger.
The overall idea is that we divide each row of a dataset by the value: sqrt( sum(square of the row) / (ncol-1) ), and then use the transpose. And yes, scale(t([email protected][[i]][genes, ]), center = FALSE, scale = TRUE)
is exactly equivalent.
For the error, can you make sure that all the var.genes can be found in your norm.data? For example:
sapply([email protected], function(nd) all([email protected] %in% rownames(nd)))
from liger.
Related Issues (20)
- Prepare for upcoming Seurat v5 release HOT 1
- Bug in Seurat's wrapper function HOT 1
- cran package archived HOT 6
- NaNs during `SelectGenes()` HOT 1
- Error on makeFeatureMatrix HOT 1
- How to improving similarity between snRNA-seq and snATAC-seq nuclei, by tuning parameters like 'k', 'lambda'? HOT 4
- Dataset specificity plot
- Issue with loading old liger object via convertOldLiger function HOT 3
- Error in `signal_stage()` HOT 4
- invalid type "list" in R_matrix_as_sparse error HOT 3
- no slot name "defaultCluster" for this object of class "liger" HOT 1
- Query on building shared factor neighborhood graph HOT 2
- Error when performing the Wilcoxon test on the peak counts HOT 1
- Error in ImputeKNN
- How can I determine the similarity scores between clusters using Liger's UINMF? HOT 5
- I cannot find joint cluster result in liger object HOT 2
- Error When Using `createLiger` with HDF5 File HOT 2
- Loading a dataset generated with 'liger' using 'rliger' HOT 4
- setting axis limits with plotGeneDimRed HOT 1
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 liger.