I'm using my results of a Differential Gene Expression from RNAseq data using DESeq2 as input data for both Pathview and topGO. I manage to get similar results for both but I am interested to know if i can use the results from one package as the input to the other (e.g. use the GO obtained from topGO to construct a KEGG pathway with pathview).
This question comes for the fact that topGO is used for microarray data and when i want to obtain the list of genes that are significant in one of the GO terms I can't do it using the printGenes function, as I'm not using a chip library (I use a custom annotation that are my Ensembl gene IDs). I am also interested in the showGroupDensity function of topGO.
So, is there any way to perform a topGO analysis and then construct the pathway with pathwview using the data from topGO?