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

[Simon Anders]

Hi Lucia

On 16/05/13 19:25, Lucia wrote:
> My counts are in fact total counts per transcript and not averages,
> my mistake in the original post

I hope you mean counts per _gene_, not per transcript. Otherwise, it is 
easy to guess what is going wrong.

Maybe explain in more detail how you obtained the counts. There are 
surprisingly many ways of getting this wrong.

You are right that filtering for PCR duplicates in RNA-Seq is rarely a 
good idea due to the dramatic impact this has on the dynamic range.

   Simon