Comments (3)
Hi Bosh - I agree that statistically the correct thing to do is to exclude
that observation (that's what the Dirichlet-multinomial would do
implicitly). Yang maybe you can comment on how you did this with
matrixEQTL?
On 28 June 2016 at 11:17, Boxiang Liu [email protected] wrote:
Hi David,
Thanks for making leafcutter available. I am wondering what your strategy
is to deal with 0/0 in sQTL mapping. I have a few thoughts but none are
quite optimal. The first one is to simply through these samples out (for
the particular intron). However, neither matrix eQTL or fastqtl will be
happy with missing data. Another thought is to consider them zero. However
this perhaps does not reflect what is really going on. The final thought is
to maybe use Laplace smoothing, making the proportion 1/N where N is the
total number of introns in the cluster.Do you have any thoughts on this?
Bosh
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#8, or mute the thread
https://github.com/notifications/unsubscribe/AET_Bhz4BHzEHNHD9BF-OfcveEXqSKqrks5qQWVLgaJpZM4JAYjS
.
David A. Knowles,
Stanford University.
E-mail: [email protected]
Web: http://cs.stanford.edu/~davidknowles/
from leafcutter.
You can try setting the value to the mean/median if not too many are
missing.
Yang
On Tue, Jun 28, 2016 at 11:21 AM, davidaknowles [email protected]
wrote:
Hi Bosh - I agree that statistically the correct thing to do is to exclude
that observation (that's what the Dirichlet-multinomial would do
implicitly). Yang maybe you can comment on how you did this with
matrixEQTL?On 28 June 2016 at 11:17, Boxiang Liu [email protected] wrote:
Hi David,
Thanks for making leafcutter available. I am wondering what your strategy
is to deal with 0/0 in sQTL mapping. I have a few thoughts but none are
quite optimal. The first one is to simply through these samples out (for
the particular intron). However, neither matrix eQTL or fastqtl will be
happy with missing data. Another thought is to consider them zero.
However
this perhaps does not reflect what is really going on. The final thought
is
to maybe use Laplace smoothing, making the proportion 1/N where N is the
total number of introns in the cluster.Do you have any thoughts on this?
Bosh
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#8, or mute the
thread
<
https://github.com/notifications/unsubscribe/AET_Bhz4BHzEHNHD9BF-OfcveEXqSKqrks5qQWVLgaJpZM4JAYjS.
David A. Knowles,
Stanford University.
E-mail: [email protected]
Web: http://cs.stanford.edu/~davidknowles/—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#8 (comment),
or mute the thread
https://github.com/notifications/unsubscribe/AE1pia39VrLMfZbYh0rDZR-BXU_Q_TlJks5qQWYbgaJpZM4JAYjS
.
from leafcutter.
That makes sense. Thank you!
from leafcutter.
Related Issues (20)
- question regarding the AS types (paper supplementary figure1)
- Error report for $bam2junc.sh
- an error about leafcutter_cluster.py HOT 4
- question regarding p-value for each intron usage
- Unable to install leafcutter R 4.2.1 HOT 8
- ENSG id and gene name not matching HOT 1
- Devtools installing LeafCutter Error HOT 5
- Delta psi is inconsistent in Leafviz HOT 1
- leafviz visualization does not show gene names HOT 1
- Error Running Differential Splicing Analysis
- error in prepare_phenotype_table.py
- installation problem HOT 3
- Empty cluster output HOT 1
- --outSAMtype BAM Unsorted ? HOT 3
- checkchrom doesn't seem to work for me HOT 1
- checkchrom issue
- Installation probelm r/4.3.1 HOT 6
- leafcutter_ds.R got error HOT 2
- Installation problem. py2.7 r3.6.0 conda install HOT 4
- leafcutter2::leafcutter-ds errors out when groups_file.txt has no cofounder columns
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 leafcutter.