[BioC] edgeR and FDR values always equals 1

[Simon Anders]

Hi

On 11/11/2010 11:44 AM, A Gossner wrote:
> While using edgeR to analysis my Tag-seq data, no matter which way I
> analyse the data common or tagwise dispersion the FDR value is always 1.
> Typical output is shown below;
[...]
>> d$common.dispersion
> [1] 4.884378

A common dispersion value of 4.8 means that your expresiion typically 
varies between replicates by 220% (that's sqrt(4.8.)). In other words, 
there is only noise and no signal in your data -- or you are doing 
something fundamentally wrong.

Look at some scatter plots, plotting the count values of one sample 
against the count values of a replicate sample on a log-log scale (or 
better, plot asinh(count) ). Do they seem to correlate?

   Simon