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Balance values interpretation #48
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hello, I have the same question, too. Did you got it? and i also wander what does a negative value of the flux mean? Thank you so much!! |
Hi, @LiuCanidk, thank you so much for your reply, and here is another question for me. In the tutorial2, the author embedded the fluxes predicted by scFEA into the scRNA-seq and preserve the sign of the fluxes. I wonder if it possible for me to use the absolute value of fluxes as I just want to focus on the amount of the fluxes as a representation for some metabolic pathways' activity but not the direction. |
I guess so. I think the sign does not reflect the direction (if so, I believe the authos should clarify this point), so you can use the absolute value. But you may carefully check the range of the absolute values for specific metabolic pathways, as they may vary too little to represent the difference of metabolic activity across cells or clusters (I note that many flux values are very small), which is visualized by the color of UMAP heatmap. So I recommend you to scale the z-score across cells or samples substituting for absolute values of specific pathways in order to reflect the variation across cells, which might be more readable in the UMAP heatmap. By the way, maybe the final correct answer should be proposed with the author. I cannot have 100% confidence...... |
Really appreciate for your reply!!!
…---- Replied Message ----
| From | ***@***.***> |
| Date | 04/13/2024 11:51 |
| To | changwn/scFEA ***@***.***> |
| Cc | Joyjoyjoyc ***@***.***>,
Mention ***@***.***> |
| Subject | Re: [changwn/scFEA] Balance values interpretation (Issue #48) |
@Joyjoyjoyc
Hi, @LiuCanidk, thank you so much for your reply, and here is another question for me. In the tutorial2, the author embedded the fluxes predicted by scFEA into the scRNA-seq and preserve the sign of the fluxes. I wonder if it possible for me to use the absolute value of fluxes as I just want to focus on the amount of the fluxes as a representation for some metabolic pathways' activity but not the direction.
I guess so. I think the sign does not reflect the direction (if so, I believe the authos should clarify this point), so you can use the absolute value. But you may carefully check the range of the absolute values for specific metabolic pathways, as they may vary too little to represent the difference of metabolic activity across cells or clusters (I note that many flux values are very small), which is visualized by the color of UMAP heatmap. So I recommend you to scale the z-score across cells or samples substituting for absolute values of specific pathways in order to reflect the variation across cells, which might be more readable in the UMAP heatmap.
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@Joyjoyjoyc |
As others have indicated previously. It is not clear how to interpret the balance values (especially the negative values). Could you maybe explain it a bit more in simpler terms?
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