enrichmentmap build command - two generic datasets not working properly

[risserlin]

specifying two datasets with the build command with generic analysis type:

two dataset files and one gmt file does not behave the same way as the interface.

I think the gmt is not being associated with either datasets or is only being set to one of the datasets.

Here are example files - gmt file - https://www.dropbox.com/s/kcnwjgr66casvhu/gprofiler_full_hsapiens_e109_eg56_p17_1d3191d_.name.gmt?dl=0 dataset1 - https://www.dropbox.com/s/xut4zxwqj3h0j0f/gProfiler_hsapiens_lab2_results_GEM_termmin3_max250.gem.txt?dl=0 dataset2 - https://www.dropbox.com/s/zksgib85yhjl4zs/gProfiler_hsapiens_lab2_results_GEM_termmin3_max10000.gem.txt?dl=0

parameters - q-value 0.001 jaccard threshold 0.35

result in the interface :

results with the same parameters but using build command -

In the build command there is no option for gmt1 or gmt2 or commongmt that I can see.

Do I have to create a mastermap for 2 datasets?

[mikekucera]

Hi Ruth, I'm getting the same results from the command and from the UI. They both look like the second screenshot above. Something else must be different in the UI settings. Can you give it another try and let me know if you can still reproduce the issue? Thanks.