[BioC] [Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?

[Simon Anders]

Hi Thomas

Forgot to add a sentence to make clear what I'm at:

On 21/05/13 21:01, Simon Anders wrote:
> The "complications" I had in mind apply to mean coverage as well as to
> reads.
[...]
> Consequently, a method which aims at getting _unbiased_ point estimates
> of expression strength is typically unsuitable as input for strength for
> differential expression testing. The point that counting for expression
> estimation and for DE testing are different tasks is subtle and often
> overlooked. Mistakes arising from this can cause strange effects.

I wanted to add: The issue I described is about which reads to use and 
which to discard when counting (or how to resolve ambiguities about 
which gene or possible mapping a read should be assigned to when there 
are several options). And this issue arises no matter whether you want 
to obtain counts or mean coverages.

   Simon