I have miRNA-seq data, and as part of the QC steps, I want to calculate the coefficient of variation between the QC samples (including inter-plate, intra-plate, and commercial universal controls) using DESeq-normalized counts. For these calculations, do I have to normalize only those specific QC samples together, or do I have to normalize these QC samples together with the rest of the other test samples? Note that not all the samples have the same miRNAs (some samples have 0 counts for specific miRNAs)
I tried both methods (normalizing only the QC samples and normalizing them with other test samples), and the CVs were different. So, I am wondering which is the correct way to give me the true variation between the QC samples?