Comments (9)
Hi,
We only used the 'unsorted' data. In addition we used the data that the authors of the original paper had used for clustering. These clusters were not published so they sent them to us. However, I'm not sure I can share these.
MAGIC settings:
npca = 100
k = 12
ka = 4
epsilon = 1
t = 9
David
from magic.
I see. Thanks for the quick reply. What do you mean by 'unsorted' data? And, maybe the authors of the original paper filtered out cells with less than 1000 reads?
from magic.
https://www.dropbox.com/s/v0v7fhf8foryacz/MAP.csv?dl=0
from magic.
Thank you David! So selecting these 2730 cells from 'GSE72857_umitab.txt.gz ', and filter out genes with no reads among these 2730 cells, then use the magic parameters you just showed us and we should re-produce the same result?
from magic.
right
from magic.
thanks!
from magic.
Hi David,
We selected 2730 cells from the raw matrix, normalized the data, did magic, and plotted gene-gene relationship. The result is very similar to the figures in your paper. Thank you for your help!
I found that in order to get similar result as in your paper, we don't do log-transformation. Is that what you suggest?
Thank you!
from magic.
that's correct. we only did library size normalization
from magic.
Thank you, the re-producing those biaxial plots were successful!
from magic.
Related Issues (20)
- Magic issue with mkl
- Suggestions for Unable to allocate 276. GiB for an array with shape (161877, 228942) and data type float64
- Magic + seurat workflow HOT 4
- Running UMAP after Magic - is it valid?
- NaN values when computing the kernel lead to inability to find t-optimal MATLAB.
- MAGIC on RNA + ATAC data HOT 5
- Error: package or namespace load failed for 'Rmagic': HOT 5
- Does it really run in parallel?
- problem running magic HOT 1
- Animate MAGIC error
- Rmagic was removed from the CRAN repository HOT 3
- magic() function error: Stuck on "Calculating PCA..." HOT 1
- ValueError: Length mismatch: Expected axis has 100 elements, new values have 10782 elements
- Name of the package confused with python-magic package
- can not put in more than 1 genes. HOT 5
- Getting 0.0 after imputation
- Option for Computing KNN with some genes, but returning whole graph
- Rmagic HOT 2
- Is it a good idea to run magic on sctransform processed data?
- Is it possible to pass a custom embedding?
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 magic.