Dear all. Could you please help me with the interpretation and transformation of topGO results. I've performed the pipeline using a set of differentially expressed genes obtained by DESeq2 on a non model organism. I would like to plot the results using a enrichment factor, or the fraction of genes presented in the dataset compared to the background. However, the GenTable function give me only the Annotated and Significant genes associated with a GO. My question is if I could determine the fraction of genes in the set by dividing the number of genes associated with a single GO by the number of genes assigned with a GO in both reference and background? For instance, for GO:0006412, annotated is 243 and significant is 72. The number of genes with assigned GO in the whole gene set is 2606 and in the differentially expressed gene set is 277. So, the fraction of genes in the test set would be 72/277 (25.99%) and in the background would be 243/2606 (9,32%). Is my reasoning correct? Thank you, Charley
If I am not mistaken, you can also obtain the column "Expected" (in addition to "Annotated" and "Significant") in the GenTable output. The quotient between "Significant" and "Expected" could be interpreted as the enrichment factor.
Thank you very much for your quick answer. It solved my question. Best