Hello, I am looking at this heatmap and I do not understand why some of the tumours are grouped with the controls, seems as if the heatmap is 'moved to the left': Top of the heatmap:
(it is a long heatmap so i upload just a section)
Bottom of the heatmap:
I tried to check on the phenotype of the samples but I found no correlations of the phenotype with this grouping.
There seem to be two tumour subgroups: one that is the biggest, and the small group of tumors that seem to be grouped with the controls. I did a t-test on the mean beta values for all the cpgs between these two groups, and it turns out there is significance among the means of these two tumour groups. I am afraid when we publish a heatmap similar to this one, we will have trouble explaining this phenomenon. Any ideas or any opinions on this? Thank you!