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

[Thomas Girke]

Hi Simon,

Because of these complications, I am sometimes wondering whether one
couldn't use for many RNA-Seq use cases coverage values (e.g. mean
coverage) as raw expression measure instead of read counts. Has anyone
systematically tested whether this would be a suitable approach for the
downstream DEG analysis? Right now everyone believes RNA-Seq analysis
requires read counting, but honestly I don't see why that is. Perhaps
the benefits of this are so minor that it is not worth dealing with a
different type of expression measure. 

Thomas

On Mon, May 20, 2013 at 11:15:04PM +0000, Simon Anders wrote:
> Dear Lucia and list
> 
> On second reading, I noticed that my previous post sounded quite 
> aggressive, which was not my intention. Sorry. I shouldn't write e-mails 
> that late at night.
> 
> Anyway: We had a lot of discussion on this list and others recently 
> about how to correctly obtain a count table for differential expression 
> analysis from aligned RNA-Seq reads. From these discussions, it has 
> become clear that this is a task with many more pitfalls than one might 
> expect at first. In microarray analysis, there is no need to do this, 
> and so read counting is a likely culprit when such discrepancies are 
> noted. This is why exact details on the procedure are so important.
> 
>    Simon
> 
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