I have been using limma to do differential analysis between two different groupings, both splitting the samples into two groups. The results for one set give approx. 100 significant genes (adj. p-value<0.05) whereas the other gives approx. 1000 significant genes. Is this suggestive that the second grouping is more "accurate" than the other? What is the best way to test this in a statistical manner. Many thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}

On Aug 3, 2007, at 8:01 AM, Daniel Brewer wrote: > I have been using limma to do differential analysis between two > different groupings, both splitting the samples into two groups. The > results for one set give approx. 100 significant genes (adj. > p-value<0.05) whereas the other gives approx. 1000 significant genes. > Is this suggestive that the second grouping is more "accurate" than > the > other? What is the best way to test this in a statistical manner. Why do you think the results are more accurate / better, just because you have more DE genes. The best result is the one that is closest to the true list of DE genes when taking the experimental . Also, if the two groupings are different, it might very well be that both lists are true at the same time. It is hard to comment on this without knowing more about what you are doing. And I would be hard pressed to come up with a situation where more DE is necessarily better (in the "more true" sense as opposed to the "I would really like a big list" sense). Kasper