I am analysing a total of four different groups and my aim is to understand what are the proteins differentially expressed in the groups and their relative fold changes.
I am carrying LFQ with a bottom up approach.
I am aware that I can use ANOVA to assess what proteins are significantly different in between the groups, while if I want to know which proteins are specifically different in each group, a post-hoc test such as Tukey test should provide this information.
My questions is the following: If I wanted to express fold change for each protein within the four groups analysed, should I use the ratio of the group with highest response against the group with the lowest response for each protein, or would you use a different approach to report fold changes within the four groups? Just to give you an example I have the following table with responses for Protein A in the different groups:
Protein Group 1 Group 2 Group 3 Group 4 Mean Fold change A 100 400 600 100 300 6
The response for each group is the mean from three replicates. So in this case should I express the fold change as 6, or do you think I should use a different approach?
Thanks a lot for your help