Entering edit mode
18 months ago
asadrahmanms
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0
Hi I have GSEA result plot. Would you please someone kindly interpret me this result. Which one is good: A, B or C and why? Or all of them are not good. I am new in this kind of analysis, and I am not sure how to interpret this. Any help would be helpful for me.
First, you should have a look at significance. Only the first pathway reached FDR<0.05. Plots are just for visualization. On the first plot, you see that genes related to the pathway tend to be concentrated on the left part of the plot, which means they are in the first rankings of your ordered datasets. As we do not know how the dataset was ranked, it is difficult to draw conclusion on how the pathway is affected by your condition (up or downregulated ?). Additionnally there is twice the same pathway (PI3K-Akt) so it is disturbing, you need to give additional information about these results
Hi thank you for your reply. 3 plot from 3 corresponding ranked list (A is top pathway from algorithm x ranked list, B is top pathway from algorithm y ranked list, and C is bottom pathway from pvalue ranked list, sorry I did not include top pathway from pvalue which looks similar to figure A). Most causal genes from algorithm ranked as top and less causal are ranked bottom, then provided into the GSEA like that. Really appreciate your help I got some understanding here.
Have a look at the detailed documentation provided regarding GSEA and how to interpret the results. Look at the section "Interpreting GSEA Results".
They also mention why using an FDR threshold < 0.25, rather than the usual <0.05. The second fundamental statistics you want to look at is the NES, where generally you would use a threshold of > |1|.
Thank you for your response. I was also looking for those threshold as you mentioned specially NES threshold. It is really helpful to know that. I will look into the resource you mentioned.