Hello all,
I have RNA seq data from 2 replicates of control and treated (say for example C1,C2,T1,T2). But when I compared the replicates separately (C1vsT1) ,(C2vsT2) there were around 1500 differentially expressed genes, but when the company combined the replicates together (all control C1C2 together vs T1T2 together) the differentially expressed genes were around 160 only. Also, the differentially expressed genes which showed up for combined replicates were different than the ones in C1TI or C2T2. Could anyone tell me what might be the reason for this?
Thanks
I have RNA seq data from 2 replicates of control and treated (say for example C1,C2,T1,T2). But when I compared the replicates separately (C1vsT1) ,(C2vsT2) there were around 1500 differentially expressed genes, but when the company combined the replicates together (all control C1C2 together vs T1T2 together) the differentially expressed genes were around 160 only. Also, the differentially expressed genes which showed up for combined replicates were different than the ones in C1TI or C2T2. Could anyone tell me what might be the reason for this?
Thanks
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