mRNAseq FPKM vs qPCR Ct does NOT correlate

sindrle · 09-24-2013, 05:38 PM

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

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09-24-2013, 05:38 PM	#1
sindrle Senior Member Location: Norway Join Date: Aug 2013 Posts: 266	mRNAseq FPKM vs qPCR Ct does NOT correlate 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