So, currently I want to do something like a comparison of micro array and RNA-seq data. In micro array, I have sample A and B1 and in RNA-seq, I have sample A and B2. I want to know the difference between B1 and B2 in terms of changes that occur from A. My method is list all DEG from microarray and check it in RNA-seq data. If the result is different (for example, in micro array it is up reg, but in RNA-seq it is not upreg) I will think of it as the difference.
My question is, is the comparison acceptable? How to check statistically the difference that occur from this comparison is biologically significant?
Thank you for your answer.