Hi,
For few of my plant samples with no biological replicates I am using edgeR.
If I use bcvvalue 0.1, I am getting >10k significantly differential expressed transcripts out of 47310 transcripts.
If I use bcvvalue 0.4, I am getting ~5k significantly differential expressed transcripts out of 47310 transcripts.
edgeR manual suggest that bcvvalue 0.4 for human.
I am not sure which to select? Because of more than 10K significant genes?
Can any one suggest me the right way?
Regards,
Manoharan