I’m looking for a metabolic pathway analysis based on VIPs from a PLS model (continuous variable). After transforming and normalizing the data, the “Select a pathway library” and “Specify pathway analysis parameters:” menus appear. As the samples are mouse blood, I’d like to use the mus musculus library (KEGG) and make a scatter plot (global test, relative betweeness centrality). However, I get an error message. Surprisingly, when I select the homo sapiens library (KEGG) for the same data set, the analysis works. Similarly, I can produce a heatmap by selecting the mus musculus library. This seems to indicate that my dataset is well supported by the application. Could someone please explain why pathway analysis doesn’t work when I select the mus musculus library (KEGG) while my dataset works for heat maps or when I use the homo sapiens library for pathway analysis?
Hello, I can’t edit my previous post so I’m reposting below taking into account the guidelines you quoted, please excuse me for not having rigorously followed it previously.
I’m looking to analyze metabolic pathways from the VIPs of a PLS model (continuous variable, see screenshot 1). I click directly on “proceed” in the data integrity check menu, and the same goes for the ‘Name/ID standardization’ menu. After transforming and normalizing the data (sample normalization = none, data transformation = log10, data scaling = auto scaling), the “Select a pathway library” and “Specify pathway analysis parameters:” menus appear. As the samples are mouse blood, I’d like to use the mus musculus library (KEGG) and make a scatter plot (global test, relative centrality betweeness, screenshot 3). However, I get an error message (screenshot 4). Surprisingly, when I select the homo sapiens library (KEGG) for the same data set and parameters (scatterplot, global test, relative centrality betweeness, (screenshot 5)), the analysis works. Similarly, I can produce a heat map by selecting the mus musculus library (heat map, global test, relative centrality betweeness, (screenshot 7)). This seems to indicate that my dataset is well supported by the application. Could someone please explain why the metabolic pathway analysis doesn’t work when I select the musculus library (KEGG) while my dataset works for heat maps or when I use the homo sapiens library for pathway analysis? The dataset is attached to this post.
Sorry, but It seems that the problem explained above is still present. I repeated exactly the procedure I described in my last post, and I still get an error message for metabolic pathway analysis (with mus musculus library KEGG) with a PLS model.
PLS with the musculus library (KEGG) works! Thank you very much!
I just have one more question, when I compare the pathway analysis results between the human library and the musculus (KEGG) library, I find the same thing. Shouldn’t there be some differences between the two?
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