`GOID Term Annotated Significant Expected weightFisher p.adj
1) GO:0007229 integrin-mediated signaling pathway 78 26 8.42 4.1E-06 0.0599 2) GO:0030335 positive regulation of cell migration 369 49 28.2 0.00042 1 3) GO:0005615 extracellular space 938 160 100.26 4.7E-09 0 4) GO:0042383 sarcolemma 73 18 7.8 9E-06 0.0082`
Above is some example of my recent topGO output. I will run classicKS and elimKS today. In regards to the weightFisher and padj values - how do the values correlate respectively? Taking both values into account what is the ranking of significance here (ordered from 1-4)?. What do padj values = 1 and = 0 indicate (are these values valid)?
Taking only padj into account, as I need to educate myself on topGOs stats like weightFisher, I would say that only 4) is significant (p-value < 0.05): 4) GO:0042383 sarcolemma 73 18 7.8 9E-06 0.0082
Do I reject the other entries? Do I ignore padj and focus on weightFisher - if so, what is significant?
I will study the vignette further however any experienced insight and additional advice (about general practices on statistical tests with topGO - fisher, classicKS and elimKS) is appreciated.
Thank you!
