I have a matrix of expression(counts) derived from 2 RNA experiments. I have combined the two experiments . I would like to normalize the data in away that at the end I have the expressions at the same scale and can do Differentially expression analysis.
What I have tried so far is using edgeR normalization method and limma package to remove the batches which failed to put the data in same scale.
Now I would like to try normalization with respect to House-Keeping genes which is new to me. I don't know how I can find those HKGs from the expression data. Is there any R package to detect those genes or I need to find them manually? If So, How should I do that?
The next step after finding the list of HKGs is the Normalization using this genes' expression where I need help too.
Thank you in advance