MS Data for enrichment pathway analysis

Question

[beslinail]

Hi all I have proteomic data of MS. I ll plan to utilize it for pathway enrichment analysis. I am focusing on using the statistics difference protein levels in data using Gene Set Enrichment Analysis (GSEA). The problem is I don't know what value(pvalue, fold change and q value) I ll use to rank the gene list and load it through the pathway software or databases

[Jean-Karim Heriche]

It should be a matter of personal preference. A p-value could be seen as a measure of how surprising the corresponding measurement is given some hypothesis on how the world works but doesn't say anything about how strong the measured effect is. On the other hand, the measured value (here fold change) tells you how strong the effect of a perturbation is. So your choice is to rank the genes by how surprising they are in your view of the experiment or by how big the effect (of treatment, disease ...) is.