Comments (3)
Hi,
First of all: awesome that you are critically inspecting the results so you know what is not working. Getting to the bottom of why Dinosaur is making mistakes on particular features is a bit of a craft, and it's hard to fix specific features without breaking others, so be warned :). My general process would be
- select target feature which is not correct
- create a test mzML with only a small region of the data surrounding the target feature
- modify the Dinosaur source with a conditional block that's triggered when processing the target feature
- add a breakpoint in that block and debug there. See if the in-process data is as expected.
- If it is, repeat at a later stage in the processing, otherwise find a way to fix the problem!
As for your setup, the fact that you use labelled data is likely to mess with the expected isotope distribution computation. To solve that it would be nice to compute averaginecorr against both labelled and non-labelled distributions, and select the best one (if some param flag was set to look for labelled features).
Hope that helps!
from dinosaur.
Hi fickludd,
Awesome and fun work. I am also seeing that the hill climbing is not picking up very abundant isotopes (several left ones). Anyway to see the centroided data as output? Also, I would like to have direct chat with you if you are available.
Hi Owen Duncan,
What software are you using to visualize the 2d map?
Thanks in advance.
from dinosaur.
@ykil Glad you like it!
What do you mean by see the centroided data as output? In general the features are the output, and these are computed on centroided data. There are examples of the centroiding algorithm in the audit trail, and I've never observed any problems with this part. This part is btw an exact clone of MaxQuant, so you would be seeing issues there as well if that was the problem.
As for direct chat, please mail me at my gmail account (I'm the first author of the paper) and describe what you want to talk about, and I can see if I can find some time.
from dinosaur.
Related Issues (14)
- Example of advParams: hillPPM HOT 1
- feature HOT 2
- Active? HOT 4
- Low performance for Orbitrap Fusion data HOT 4
- How to change advanced paprameters? HOT 2
- DIA data will work? HOT 6
- MS2 mapping? HOT 1
- Error in Maven install HOT 1
- Match between runs HOT 5
- Maven error when compiled as dependency within Quandenser HOT 5
- IntensitySum HOT 2
- TIMS-TOF spectra HOT 1
- FWHM output 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 dinosaur.