SVA on RT-PCR verification of RNA-Seq data

Question

[henry-keen]

We performed an RNA-Seq experiment and used SVA to correct for potential batch effects. We are now doing RT-PCR verification of those RNA-Seq results. Is there any way to apply the SVs identified from the RNA-Seq data to do correction on the RT-PCR data?

[ATpoint]

Is there even evidence that the PCR data suffer from any comparable batch effect, I mean after all it is a completely different type of experiment?

[henry-keen]

Good point. Thanks for your comment. I can use removeBatchEffect from the Limma package to do the correction on the Ct values (or delta Ct) from the qPCR. The question is whether or not it is valid to assume that batch effects present in the RNA-Seq experiment are also present in the qPCR experiment. Of that, I'm not certain. The same RNA was used as input, but otherwise they are, as you say, completely different experiments.