I have used galaxy to study differential expression of gene for my experiment while my lab-mate has been using R for the same. The amount of significant genes obtained by me is far less than what he has got through R. I would really like to know the cause for this discrepancy in data obtained. What measures could I take to cut down on the difference between the two methods?
Regards,
Shruti
Hi,
as a first step, you can take note of all Galaxy tools you used in the process and compare that list to steps your colleague took.
You can also inspect each Galaxy tool’s command line package dependencies at the very bottom of each tool interface. Write down the names and versions there and, again, compare them to tools your colleague used.
Finally, for every dataset you’ve created in your analysis history, you can click the i icon to get to a details page, which will, among other things, allow you to see the exact command line instructions that have been performed to get this dataset. Again, compare these to what your colleague did.
Cheers,
Wolfgang
1 Like