Forum: RNAseq validation using qPCR
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gravatar for phalange.re
4.1 years ago by
Australia
phalange.re0 wrote:

Hi guys,

I've run qPCR validation of my RNAseq data to address the comments of one of the reviewers of my manuscript. I'm just a bit confused on how to compare the data from RNAseq and qPCR. Comparing the fold changes (as seen in many papers) doesn't seem right to me. I've used edgeR for my RNAseq DGE analysis and 2^-DeltaCq (using geo mean of three reference genes) for the qPCR data. These data don't seem comparable based on how different these analyses are. Could you please let me know how do you guys usually compare these two methods? Is fold change comparison really OK?

Thanks a lot!

rna-seq next-gen forum • 2.1k views
ADD COMMENTlink modified 4.1 years ago by Sam2.4k • written 4.1 years ago by phalange.re0
1
gravatar for Sam
4.1 years ago by
Sam2.4k
New York
Sam2.4k wrote:

The way I do it is to correlate the RNA Seq count with the Delta CT values (or the Delta CQ in your case?). If you have a high negative correlation, it means that your RNA Seq count is more or less representative of the actual mRNA concentration. Also, if you are interested in seeing if the fold change, or more precisely, the significance of difference observed in RNA Seq can be validated by the rtPCR, then you can follow instruction of this paper

ADD COMMENTlink written 4.1 years ago by Sam2.4k
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