Comments (3)
linqiaozhi
commented on June 10, 2024
Hi @Winnie09, we use the normalize_data() function to convert the count matrix into a library size and log transformed matrix. We have not explored the effects of not normalizing or not doing the log transform, however.
The output can be considered to have the same "transformation" done to it as the input data. The alra() function itself does not actually do any normalization, but if the input data was normalized, then the imputed data will have roughly the same distribution.
from alra.
Winnie09
commented on June 10, 2024
This is very helpful. Thanks a lot!
On Mar 20, 2019, at 10:01 AM, George Linderman <[email protected]<mailto:[email protected]>> wrote:
Hi @Winnie09<https://github.com/Winnie09>, we use the normalize_data() function to convert the count matrix into a library size and log transformed matrix. We have not explored the effects of not normalizing or not doing the log transform, however.
The output can be considered to have the same "transformation" done to it as the input data. The alra() function itself does not actually do any normalization, but if the input data was normalized, then the imputed data will have roughly the same distribution.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AV0rVZ3XrY88kYNN4jKZXNHRpD4rexmFks5vYj8ugaJpZM4b6nAB>.
from alra.
chatterjee89
commented on June 10, 2024
Hi @linqiaozhi I have a quick question related to this one:
Would you recommend applying ALRA to impute scaled data or raw data in the count matrix?
Thank you so much for the question and the software.
FYI, I'm applying this on scRNA Seq data being analyzed on Seurat.
Regards,
Deep
from alra.
Related Issues (20)
- Best Practice for imputing big data-sets HOT 2
- Can I use ALRA imputed matrix to perform the `Find Marker Gene` step ? HOT 2
- Tips for larger matrices? HOT 3
- During FindVariableFeatures after ALRA output, count slot is empty?
- Error in asMethod(object)
- GetAssayData(pbmc, slot = "counts") gives 0 x 0 matrix HOT 1
- Run ALRA in Seurat v4.1.0
- Imputation before other QC steps?
- ALRA and Seurat HOT 1
- Need to deal with R 4.2.0 HOT 5
- alraSeurat2 FUNCTION NOT FOUND!!!! HOT 3
- Final proportion of non-zero values is large. HOT 2
- Running ALRA with multiple samples HOT 10
- Differential expression HOT 5
- Provided normalized function HOT 4
- Imputing integrated data HOT 1
- Input data structure HOT 1
- big data set and K HOT 2
- Input format (genes as rows?) 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 alra.