about cufflinks

[Raa]

Hi
Can cufflinks be used to find differentially expressed isoforms between two different groups samples?. eg. 20 tumors each from two groups.

[mrfox]

You can run cuffdiff directly to compare the two groups.

[Raa]

Thank you.
How reliable cuffdiff is in this case. I read that it uses student t test for this task. It will be good for replicates or 1 to 1 comparisions.
Does cuffdiff uses any non parametric metric test (eg. U test) for comparing two large groups. For example, to find significant differences in alternative promoter use or isoforms differences between 20 tumor from males and 20 tumors from females. For this student t test is not a good option.