[BioC] edgeR on microRNA data

[Gordon K Smyth]

On Mon, 3 Oct 2011, Helena Persson wrote:

> The tagwise dispersions (cds1 <- estimateTagwiseDisp(cds1, prior.n=1, 
> trend=TRUE, prop.used=0.3, grid=FALSE)):
>
>   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
>0.09599 0.18370 0.24550 0.28160 0.31190 2.23000
>   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
> 0.1022  0.1894  0.2534  0.2916  0.3183  2.1890

A small number of the dispersions are alarmingly high.  Have you filtered 
the gene list as I suggested?  This may remove the "variance outliers".

Does a plot of the dispersions versus abundance suggest that the trend is 
smooth?

Best wishes
Gordon

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