Hello!
I want to kindly get advice on a method I am using for showing gene expression on a heatmap.
I have three groups:
- Negative Control (4 samples)
- Control with injury (4 samples)
- Treatment with injury (4 samples)
I took the intersecting significant genes (padj) from two comparisons:
- Treatment vs Control (Wald Test)
- Control vs Negative Control (Wald Test)
I plotted these intersecting genes in a heatmap for the normalized counts for each sample within each group. So we have 12 columns in total, 4 column for each group.
The results show that the gene expression for the treatment and negative control are similar and opposite to the control. This suggests that the treatment has altered gene expression in response to injury to be similar to the negative control. Basically, the most significant, overlapping genes are similarly expressed in treatment and negative control, and are oppositely expressed in control. Thus, the treatment has some sort of plausible effect.
Does this approach make sense? Is it correct? Any advice is greatly appreciated.
Thank you!
