I would like to know your opinions about the correlation I obtained between qPCR and RNA-seq for 8 genes, two of them being reference genes. The r2 is good but I worry that qPCR FC are not as high as in RNAseq. It could be:

- Normalisation bias in RNAseq analysis: normalisation was performed because ex-vivo sample had 40% of eukaryotic RNA.

- Bias in library preparation, PCR step

- Other

Here are the correlation analysis and the technical analysis results:

https://drive.google.com/file/d/0B8-ZAuZe8jldQnEzcThkOXlkNWc/edit?usp=sharing

https://drive.google.com/file/d/0B8-ZAuZe8jldYmZaSnZxMFRuVWs/edit?usp=sharing

Thanks for your help.

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