[BioC] edgeR for data combined from different studies and/or platforms

[Simon Anders]

Hi

On 18/03/13 18:07, Ryan C. Thompson wrote:
> It sounds like the two cancer projects are essentially independent. What
> do you hope to gain by combining them? As far as I can tell, the main
[...]

Ryan, I think you are too optimistic here. Santos wrote:

>> Different research teams are handling the work for the two different cancers

So, if I understand this right, then Santos has transcriptome data for 
one cancer type obtained from one team, and for the other cancer type 
from the other team. In this case, any comparison between the two cancer 
types is completely confounded with technical differences and hence 
invalid, and no statistical method will change this.

So, just to clarify: Ryan's answer is correct, of course, but he assumed 
that each of the two team provided data for both cancer types, which, I 
think, is not what Santos meant. Or is it, and I was too pessimistic?

   Simon