Comments (3)
Hi @jakob-wirbel,
Thank you very much for catching this! The package will be updated shortly to fix this BUG!
Best,
Huang
from ancombc.
Hi @lakerwsl,
Thanks for posting your question! In order for me to better dig into the problem, may you please share with your codes and a mock dataset (with all confidential information marked)?
Thank you,
Huang
from ancombc.
Hey hey 👋
i ran into the same problem and i think i found the reason for the error 😄
If you have a single metadata variable (basically, only the group label) AND you would remove samples with the minimum library size cutoff, this part of the code will return the metadata as a vector, not as a data.frame:
# Discard samples with library size < lib_cut
lib_size = colSums(feature_table, na.rm = TRUE)
if(any(lib_size < lib_cut)){
subj_del = which(lib_size < lib_cut)
feature_table = feature_table[, - subj_del]
meta_data = meta_data[- subj_del, ]
}
I think it could be fixed very quickly by changing the line to:
meta_data = meta_data[- subj_del, , drop=FALSE]
Cheers
from ancombc.
Related Issues (20)
- Additive log-ratio on counts vs proportions
- ANCOM_BC2's Global test approach?
- passed_ss_ not found HOT 2
- R session aborted while running ANCOMBC2 HOT 2
- Interpreting negative lfc values for "intercept" in primary result
- Installing ANCOMBC HOT 2
- Continuous variable as main variable of interest
- Different results with ancombc2 depending on the order of the taxa
- Visualization the output of ancombc2
- Pseudo-count sensitivity testing when no pseudo-counts are added
- Error in { : task 1 failed - "values must be length 1, but FUN(X[[2]]) result is length 0"
- Help with ancombc2 analysis with repeated measures
- Extract normalised counts for linear models outside of ANCOMBC?
- Failure to install ANCOMBC neither windows nor Ubuntu HOT 1
- global test and pairwise comparisons giving pvals of all NA or all 1
- Feature Request: Support for Using Taxa as Explanatory Variables in ANCOMBC2
- "Error: subscript contains invalid names" when running ancombc2 HOT 1
- Interpreting error when running ancombc2 function: Error in is.infinite(o1) : default method not implemented for type 'list'
- NAs and 1s in ancombc2 primary result table HOT 1
- object 'passed_ss_age' not found
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 ancombc.