I have a kind of replicates for three samples from two RNAseq works. Two RNAseq works mean I performed one RNAseq earlier, and the other RNAseq around 3 month later. I'm not sure If I can say this is biological replicates. Probably it is.
The RNAs was prepared from the same cell line. It means that the source of two RNAs are the same. But each sample was in different condition each like below.
RNAseq works-----Condition1---------Condition2-------Condition3 First RNAseq-------RNA-Sample1-----RNA-Sample2-----RNA-Sample3 Second RNAseq----RNA-Sample1-----RNA-Sample2-----RNA-Sample3
From pearson's correlation, the coefficient are 0.92 (0.80), 0.98 (0.96), 0.98 (0.96) for sample1, 2, 3, respectively when expected count (TPM value) was used.
In theory, two samples in the same condition are the same, and the expression profiles are supposed to be the same with almost coefficient 1. But, I understand technical variance.
From this, my opinion is that I can use the replicated data for sample 2 and sample 3, but I'm not sure about replication for sample 1.
Considering the coefficients of sample 2 and 3, I think technical variance didn't affect a lot between two RNAseq works. If the way I think is wrong, please point it out.
Is it OK if I think sample1 is replicated and use the data for the further analysis with that coefficient score? or Do I have to discard it?
Plus, is there any other reliable or relevant method to check replication?
I'm not very new, but don't have enough knowledge and experience in this field. Looking forward to good comment and advice.