RNA-Seq vs qRT-PCR

[nareshmvr]

I am attaching a figure based on assessing qRT-PCR vs Dual-RNASeq for selected Genome1 genes (black circles) and Genome2 genes (red circles).

I have analysed the correlation by Spearman Rank Order Correlation analysis:

Correlation Coefficient: 0.727
P Value: 0.00946
Number of Samples: 11

So, overall there is a significant correlation between the two datasets.

BUT, there is something slightly strange going on here. For Genome1, RNASeq seems to underestimate the changes in gene expression compared with qRT-PCR. Genome-2, it is the opposite - RNASeq overestimates gene regulation.
I have absolutely no idea why RNASeq should specifically underestimate Genome-1 gene regulation. please give your valuable suggestions in interprating for this qRT-PCR Validations

[nareshmvr]

Dear All,

Am still wondering about this issue , I think my question is not unclear , Please suggest me if there are any possible ways to debug my issue.