RNA seq data validation with qPCR: compare log Fold change vs Fold change?

Question

[micromira]

I sent my RNA seq for analysis to our collaborators, who returned me data in format: log fold change/FDR/pValue.

I took a gene which is up-regulated in treated sample, LogFC= 1.2, FDR, pValue < 0.05 and run validation by RT-PCR.

Using ddCt method I got 1.3 Fold change difference.

How do I compare 1.2 LogFC (RNA-seq) to 1.3 Fold change (RT-PCR) to validate that my gene is indeed up-regulated?

Answer 1

[Devon Ryan]

2^1.2 = 2.3, so the value you found is much smaller. I'm assuming that the ddCt was ~0.38, since that equates to a log2FC of 1.3 (assuming 100% probe efficiency).

BTW, you don't need to compare the fold-changes to demonstrate up-regulation. You look at the p-value of the RT-PCR results and the direction of the change to confirm things. The magnitude of the change is rarely identical.