Comments (5)
from hyper.
Hi, yes that is correct.
from hyper.
To add to that, the background depends on the assay. E.g., if you use an Affymetrix microarray that measures 13,000 features, then 13,000 is the background. If you use a protein array such as SomaScan measuring, say, 3,500 proteins, then 3,500 is the background. If you use RNAseq, than yes, the background is the number of transcripts in the transcriptome (i.e., the number of transcripts RNAseq can conceivably detect). —ste
…
On Aug 3, 2020, at 4:17 PM, anfederico @.***> wrote: Hi, yes that is correct. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACIAGH7VCIQHLLSYZ5XJQQLR64LOLANCNFSM4OVFCTFA.
I see. Thank you.
from hyper.
I will leave this issue open for a bit as this is a FAQ.
from hyper.
As a reference broad's msigdb sets the background to 40786 for their online tool:
from hyper.
Related Issues (20)
- Error in conexion HOT 1
- quiet
- reactable should be "wider" HOT 1
- Enrichment maps unable to export in a .tiff format HOT 2
- Duplicated gene symbols in the output of msigdb_download HOT 6
- sizes argument in hyp_dots function HOT 1
- error in GSEA about weighted signatures HOT 1
- How to get signetures enriched in a pathway? HOT 1
- hypeR-dot plots with KS test should incorporate directionality information
- KS with mx.diff=TRUE (GSVA-like)
- .check_overlap returns a fraction, not a percentage HOT 1
- Error in hyp_hmap HOT 2
- X-axis and Outputting Gene Overlap Size HOT 2
- rctbl_build does not work with method="ks" HOT 1
- .kstest needs to match ks.test (modulo the sign)
- MSigDB C7 retrieval fails
- rgsets does not support proper object "duplication" by value
- Hits names should be quoted (like in the csv format)
- Pushing to upstream on Bioc
- multihyp dot plot significance legend is not showing properly (solution included) HOT 3
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 hyper.