I have several datasets of untargeted metabolomic data from metabolon. Previously, when I uploaded the datasets I would normalize the data: "mSet<-Normalization(mSet, "MedianNorm", "LogNorm", "ParetoNorm". This worked as of a couple weeks ago. When I do it now I keep getting an error message that “no hits can be found.” This occurs even just with log-transforming the data. I’m not sure why this is now causing an error.
There are many updates recently. I would suggest to pay attention to the previous steps (filtering, missing values) - as the default parameters could be different. Otherwise, please follow our post guide.
Thank you for the response. I am new to doing metabolomics and have the course + Pro package that I am going to work through. Unfortunately, I cannot upload the data file since it is the Metabolon excel file. So, I’m not sure how helpful this will be.
When performing the pathway analysis, I upload the metabolon sheet. Under “data processing information” the same “errors” exist as previously: “Other special characters will be stripped” and “15 features with a constant or single value across samples were found and deleted.” I proceed through the “missing compounds.” Selecting:
Sample normalization- none
Data transformation- Log transformation (base 10)
Data scaling- none
This does not demonstrate a histogram if I want to view results (as it previously did and does if I choose variance stabilizing normalization). When I proceed with pathway analysis parameters:
Visualization method- scatter plot
Enrichment method- Global test
Topology measure- Relative-betweeness center
Reference metabolome- use compounds in the library
library- mus musculus (KEGG)
Then I get: “No hits in the selected pathway library”
If I proceed with: Sample normalization- none
Data transformation- Variance stabilizing normalization
Data scaling- none
When I run this- I get similar pathway results as my previous run; however, many metabolites are excluded when they were previously included. I was specifically trying to look at some of the metabolites.
I am not clear about which tool you are referring to. The pro is a stable release - it is literally frozen in time until next stable release. In pro version, you can save/resume your project, no need to re-upload your data everytime. Please clarify