cuffdiff significantly differently expressed genes

[Richard.Y]

I got too few significantly differently expressed genes between two samples, was something wrong. and how did cuffdiff call a gene significantly differently expressed

[chadn737]

1) How do you know its too few?

2) "two samples" do you mean multiple biological replicates of two conditions or only two samples? It makes a big difference.

[Richard.Y]

1）I got just 68 genes significantly differently expressed
2) one is cancer cell line,the other is normal tissue

[Richard.Y]

1) How do you know its too few?

2) "two samples" do you mean multiple biological replicates of two conditions or only two samples? It makes a big difference.

1）I got just 68 genes significantly differently expressed
2) one is cancer cell line,the other is normal tissue

[chadn737]

1) Why is 68 too few?

2) So you have only two samples, no replicates?