I'm stuck with something and would love your help.
I'm a biologist and I'm trying to see if some genes are upregulated or downregulated in a study. The genes are PRMT1-9 and CARM1. I've performed marker analysis and downloaded IGV (as David from insilicodb earlier suggested me) and I'm trying to visualize the results but I cant interpret them. Here's my question:
In heatmaps, the upregulation and downregulation of genes is defined on the basis of color intensity, I know that from theory. But where is the reference/standard line to which should we be comparing all the sample color lines in order to see if in that sample, that particular gene has been up-/down-regulated? I'm attaching a screenshot from IGV as well.
Please reply at the soonest.