I have done qPCR to check for differential expression of my target genes. I want to compare control (healthy donor stem cells) to different developmental stages (pro B & pro T cells from different healthy donors) and cancer cell lines that match to stem cells and the developmental stages.
Of note is the fact that I have 4 samples of healthy donor stem cells and 6 from pro-B (different donors) and 6 from pro-T (different donors). The samples in all the groups come from completely different donors.
My questions are: 1. Whether I can have different number of samples across different groups? 2. If so, what kind of statistics could I apply to get a significant result? 3. Does it make sense to include the cancer cell lines (though they do match the stages of the healthy donor samples)?
Any help will be appreciated. Many thanks, V