Question: RNA seq data validation with qPCR: compare log Fold change vs Fold change?
gravatar for micromira
5.3 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 • 3.7k views
ADD COMMENTlink modified 5.3 years ago by Devon Ryan98k • written 5.3 years ago by micromira0
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k 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 5.3 years ago by Devon Ryan98k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1258 users visited in the last hour