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Old 08-29-2011, 06:12 AM   #2
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Originally Posted by shilez View Post
However assuming when analyzing tumor samples in a few cancer subgroups, do samples in the same subgroup count as "biological replicates" too?
Of course.

Particularly does the overdispersion model in DESeq statistically sound for a potential more variable samples within a subgroup?
Yes. (Please have a look at the development version, as we made quite some changes.)

This is not to say, however, that you are likely to find much if you compare cancer subgroups and have only a few samples per group. Precisely because the variation is so large you need very many samples to have enough power to find significant differences. Furthermore, pairing samples with normal tissue from the same patient (and using GLMs for the analysis) reduces the variability.

See also this thread:
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