Cuffdiff on two sample RNA-Seq

[hollandorange]

Hi All,

I have two RNA-Seq samples: 1 control and 1 disease. And I apply Cuffdiff to detect the differentially expressed genes. And here are questions:

(1) since there are only two samples. does the p-value or q-value still make sense?

(2) I noticed that if a gene is express in one sample (for example FRKMa=10) but not in the other one (FRKMb=0), then it is not significant according to the p-value. Is it always true? There are about 2k this kind of genes, how to handle them?

Best wishes
Yanju

[NicoBxl]

(1) no. only one sample per group is not statistically enough. you can not conclude anything with this type of experiment.

(2) yes it's normal that you're p-val is not significant with two sample. even if the difference between the two FPKM is big.