Dear Users,
I have a 2vs2 comparison model for Mouse data. I have aligned them with tophat2 and I am trying to find differential expression via Cuffdiff. I have a question for interpreting the Cuffdiff result. There are hardly 10 genes which pass the significance (FDR) using Cuffdiff. The other genes although are interesting and have a good p.value but have a very bad FDR . Do you trust those genes?. Also, some of the genes are very lowly expressed say 0.004 in one condition and 0.04 in other and will have a great fold change and p.value. I am having a tough time to interpret the results as I am new to this field .
I will highly appreciate the expert opinions in this case.
Awaiting your replies.
Thanks,
Himanshu
I have a 2vs2 comparison model for Mouse data. I have aligned them with tophat2 and I am trying to find differential expression via Cuffdiff. I have a question for interpreting the Cuffdiff result. There are hardly 10 genes which pass the significance (FDR) using Cuffdiff. The other genes although are interesting and have a good p.value but have a very bad FDR . Do you trust those genes?. Also, some of the genes are very lowly expressed say 0.004 in one condition and 0.04 in other and will have a great fold change and p.value. I am having a tough time to interpret the results as I am new to this field .
I will highly appreciate the expert opinions in this case.
Awaiting your replies.
Thanks,
Himanshu
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