qPCR , H&E, IHC for Influenza is not correlated - (Jun/25/2014 )

Dear all. 

I have 3 data representing virus characterization, qRT-PCR, H&E and IHC . They are not correlated together although being from same animal 

What might be explanation 

1.) qPCR gives data on RNA level, immunostainings on protein level. They need not be correlated (protein half-time could be a confunding factor for instance)
2.) Methodical problems, e.g. problems with antibody penetration in IHC

Can you give details -where was the expression higher / lower etc. ?

H&E and IHC are not usually very quantitative, more of a qualitative process... what is the actual problem - how are they not related?

Thanks, I just wonder as qPCR data not always correlated with IHC