Hi all,
I am using edger to find DE genes among two time points (P7, P28) compared with control. In my experiment, 6 cows were subjected to treatA and 5 cows were subjected to treatB. I have the miRNA seq data for control, P7 and P28 of each cow.
Now My Question is that:
The first time I got the DE genes of treatA (P28 vs control, P7 vs control) by just importing the seq data of the 6 cows in treatA to EdgeR. (I perform the same work for treat B separately.)
The second time I imported all the seq data of the two treatments together into Edger and I still could get the DE genes for treat A and treat B. (In this way, I can compare the effects of the two treatments)
HOWEVER, the results from the two approaches for the same treatment are different. I understand that the normalization factor changed when the data of the two treatments were put together.
BUT which one is more reliable? Should I analyze the DE genes of two treatments separately or together?
I am using edger to find DE genes among two time points (P7, P28) compared with control. In my experiment, 6 cows were subjected to treatA and 5 cows were subjected to treatB. I have the miRNA seq data for control, P7 and P28 of each cow.
Now My Question is that:
The first time I got the DE genes of treatA (P28 vs control, P7 vs control) by just importing the seq data of the 6 cows in treatA to EdgeR. (I perform the same work for treat B separately.)
The second time I imported all the seq data of the two treatments together into Edger and I still could get the DE genes for treat A and treat B. (In this way, I can compare the effects of the two treatments)
HOWEVER, the results from the two approaches for the same treatment are different. I understand that the normalization factor changed when the data of the two treatments were put together.
BUT which one is more reliable? Should I analyze the DE genes of two treatments separately or together?
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