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

[Ryan C. Thompson]

I was hoping that maybe both studies included both cancer and control 
samples, so that the control samples would allow inter-study technical 
differences to be disentangled from experimental effects.

On Mon 18 Mar 2013 10:36:06 AM PDT, Simon Anders wrote:
> 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
>
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