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?
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written
by
micromira •
1 answer
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.
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written
by
Devon Ryan
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