Question: RNA seq data validation with qPCR: compare log Fold change vs Fold change?
gravatar for micromira
5.1 years ago by
micromira0 wrote:

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 upregulated in treated sample, LgFC= 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 LgFC (rnaseq) to 1.3 Fold change (RT-PCR) to validate that my gene is indeed upregulated?


rna-seq rt-pcr • 3.5k views
ADD COMMENTlink modified 5.1 years ago by Devon Ryan97k • written 5.1 years ago by micromira0
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Devon Ryan97k
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