I want to show my proteomics data (protein abundance) by heat-map. I have 1 control and 4 treatment conditions. But I don't know how exactly I can prepare data for heatmap. Actualy, I've calculated fold changes for each sample by dividing protein abundance of that sample to protein abundance of correlated control. Then I calculated log 2 for fold changes. Is it the right way to calculate fold change? If yes, the heatmap shouldn't have control, and it will be just for representing treatments. Right? After clustering I don't know how I can interpret it. Is it enough to represent just similarity by clustering? Or I am expected to eliminate or change some of my data according to the result of clustering?
Thanks in advance Zahra