Entering edit mode
Hi, I'm sorry to be so naive in the bioinformatics world. I have sequenced my samples in multiple plates and now I do not understand the best way to normalise. I selected my samples from the plates, merged the samples and then proceeded to normalise using edgeR to minimise the effect between the plates. But I am not sure if this is the best way. Do you have any tips or articles that refer to this problem and explain the best way to normalise?
Thank you very much.
What are "plates"? You mean sequencing runs? Have the libraries been prepared the same time or in a balanced / batch-aware fashion? Add some metadata to illustrate the layout.