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

[Lucia]

Dear Simon,

To obtain my count matrix I use each Ucsc gene model as one " transcript", I limit my comparisons with the microarray data to those Ucsc gene models that have a unique RefSeq match with an Affy probe set 

Regarding multiple testing, I guess there is no reason why I can't use the uncorrected pvalues produced by DESeq and run locfdr right?

Thanks for the help
Lucia

Sent from my iPad

On May 16, 2013, at 3:02 PM, Simon Anders <anders at embl.de> wrote:

> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor