I measured the gene copy number of a same sample (genomic DNA) twice last month and this month. The values are 3.8 and 5.9. I wonder whether this variation is normal. How large the experimental variation is considered acceptable.
It's going to depend very much on your question and if you are at the "extreme end range" of detection for your assay or not.
What are you using as a reference to interpolate your data? I'm assuming it's a standard curve. If the efficiency is 95%-105% and the R-squared value shows little technical variation, then the data are what they are.