Closed Kai6662 closed 1 year ago
@Kai6662 thanks for reporting this
Please describe your OS environment, software package, so that we can look into it
Hi,
My OS environment is SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux; my software is R; and the package is piano. Piano package can do reporter metabolites analysis using Model.xml. Then I tried to load mouse.xml using loadGSC function.
Best Kai
may I ask if the loadGSC function is to open a genome-scale model?
Based on piano vignette, loadGSC function is to load a gene set collection from a genome-scale metabolic model. It looks like the function included open the model and collect gene set.
I'm afraid this function cannot open a model. Maybe contact piano support to figure this out
Based on the documentation of loadGSC
, in principle loading a model should work. So I'm wondering now if perhaps it has to do with some implicitly expected gene annotation.
Do you know some alternative reporter metabolites analysis tools? So that I can use your mouse-GEM model well. I only knew piano can do that.
sure, we'd like help
Could you recommend me a software to do reporter metabolites analysis using your mouse model? I would appreciate it.
I think piano is good for reporter metabolites analysis.
To extract GSC from MouseGEM, you may try the following code and this repo:
# Load MouseGEM from your local computer after cloning the repo
load('../Mouse-GEM/model/Mouse-GEM.mat')
# Extract MouseGEM GSC after cloning and installing the GeneSetAnalysisMatlab repo
extractMetaboliteGSC(model, true, 'mouseGSC.txt')
Then the "mouseGSC.txt" file can be used with piano for downstream analysis.
Thank you so much! It is working!
good to know :-)
feel free to reopen
Description of the issue:
Error in loadGSC("/mnt/workspace_dierickx/kcui/mouse-gem/Mouse-GEM/model/Mouse-GEM.xml") : no gene association found
Hi,
I am using mouse-GEM model. I load xml file using loadGSC function in R. But there is no gene association found.
Do you know what is the problem?
Thanks in advance.
Kai