mRNAseq FPKM vs qPCR Ct does NOT correlate

[sindrle]

Hi!
I did Pearsons correlation on a set on genes from mRNAseq and qPCR, the result was terrible!
Here are some examples (see attachments also):

IL6:
t = 1.2481, df = 22, p-value = 0.2251
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.1631711 0.5984672
sample estimates:
cor
0.257152

Adiponectin:
t = 1.3771, df = 22, p-value = 0.1823
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.1372804 0.6152003
sample estimates:
cor
0.2817174

I used Tophat2 + Cuffdiff2 to get FPKM.

Can somebody shed some light over this?

Thank you so much!

IL6-pre.pdf
ADIPOQ-pre.pdf