I was taught and everywhere in the tutorials is written that after the normalization it is preferable that the curves look the same. However, if we have two conditions, one where is nothing expressed and another where all genes are highly expressed then according to this logic I can lose all significant expressions because the curves will look the same. What should I consider instead? Should be the shape the same and it is ok if the some curves are higher and anthers not?
Beneath are the square root of the normalized values. The shape is the same, however they are of different height and do not correspond to the initial experiment conditions