qPCR and HT-PCR inconsistency

Question

[SushiRoll]

Dear all,

I hope this is the right place to make this question, otherwise I would really appreciate if you could point me in the right direction. I did an HT-PCR (chip based) for a couple of genes and then measured a subset of them using qPCR. My problem is that, even though I was expecting differences between the techniques due to their nature, I get very different values, the relative abundances for each gene between the two techniques varies in several orders of magnitude. Copy number is either greatly overestimated or underestimated with HT-PCR depending on the gene. Does anyone have an opinion/experience on this?

Thanks!!