Hi! I am doing a meta-analysis on two groups and I would like to know how to change the order of comparison such that the upregulated genes would be more related to group 2 than group 1? I tried to format my dataset into case (i.e., group 2) - control (i.e., group 1) but the results show that the upregulated genes are up in group 1 and down in group 2 (when seen in the ORA heatmap). Is there any way to reverse this order?
The comparison order is likely based on alphabetic order by default, and you can play with labels to trick computer. For instance, using “Control - Case” compared to using “Control - Disease” for “Group 1 - Group 2” will have opposite effect based on alphabetical order
As I understand, you currently have FC = CTRL/CASE, so genes that are higher in case than in control show up as a negative log2FC but you want to reverse to CASE/CTRL so that they are positive. If using the ‘specific comparison’ option in differential analysis, simply switch the order of the two groups in the dropdown:
So, instead of “Control vs. High”, switch to “High vs. Control”, this will reverse the numerator/denominator for the fold-change calculation.
Hi! Thank you, this works!