i am am experiencing some issues with my qpcr results. I am working on an area in the genome which is supposed to be a deletion. The ct value for this gene of interest is consistently 18-19 ct in my control samples.
the problem is in my housekeeping gene. The amplification curves for the triplicates are all between 0.2 ct of each other, but between samples, the Ct values ar between 20-23! This is a huge discrepancy and I am very worried, as the analysis shows an amplification so instead of a deletion.
why is this happening, and can I still use these results when working on cnv analysis? Btw, these are for the control samples.
any ideas would be much appreciated!